3H02

2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella typhimurium.

PDB DOI: https://doi.org/10.2210/pdb3H02/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-08 Released: 2009-04-21
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.169
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella typhimurium.

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 196 kDa
Atom Count: 13,009
Modelled Residue Count: 1,557
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Naphthoate synthase	A, B, C, D, E A, B, C, D, E, F	288	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: menB, STM2307 EC: 4.1.3.36
UniProt
Find proteins for Q7CQ56 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CQ56 Go to UniProtKB: Q7CQ56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7CQ56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth F] MOL2 format, chain G [auth A] MOL2 format, chain M [auth F] mmCIF format, chain G [auth A] mmCIF format, chain M [auth F]	G [auth A], M [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain M [auth F]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain N [auth F] SDF format, chain O [auth F] SDF format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] MOL2 format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth F] mmCIF format, chain H [auth A]	H [auth A] I [auth B] J [auth C] K [auth D] L [auth E] H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], N [auth F], O [auth F]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain N [auth F] Focus chain O [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.169
R-Value Observed: 0.171
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m33h02

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.897	α = 90
b = 132.819	β = 90
c = 151.791	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary