4K1W

Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and d-mannonate

PDB DOI: https://doi.org/10.2210/pdb4K1W/pdb
Entry: 4K1W supersedes: 3R4E

Classification: ISOMERASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-04-06 Released: 2014-04-09
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.184
R-Value Work: 0.157
R-Value Observed: 0.158

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the A314P mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and d-mannonate

Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 190.62 kDa
Atom Count: 13,572
Modelled Residue Count: 1,549
Deposited Residue Count: 1,672
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein	A, B, C, D	418	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 1 Gene Names: Saro_3675 EC: 4.2.1.8
UniProt
Find proteins for A4XF23 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XF23 Go to UniProtKB: A4XF23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4XF23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS2 Query on CS2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D]	F [auth A], L [auth B], Q [auth C], X [auth D]	D-MANNONIC ACID C₆ H₁₂ O₇ RGHNJXZEOKUKBD-MBMOQRBOSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Y [auth D]	G [auth A], M [auth B], R [auth C], Y [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain Y [auth D]
PDO Query on PDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	AA [auth D], J [auth A], O [auth B], V [auth C]	1,3-PROPANDIOL C₃ H₈ O₂ YPFDHNVEDLHUCE-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain V [auth C]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	H [auth A], I [auth A], S [auth C], T [auth C], Z [auth D]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain W [auth D]	E [auth A], K [auth B], N [auth B], P [auth C], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.184
R-Value Work: 0.157
R-Value Observed: 0.158
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.223	α = 90
b = 165.363	β = 90
c = 167.197	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-09

Deposition Author(s):

This entry supersedes: 3R4E

Revision History (Full details and data files)

Version 1.0: 2014-04-09
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description