3UNV

Pantoea agglomerans Phenylalanine Aminomutase

PDB DOI: https://doi.org/10.2210/pdb3UNV/pdb

Classification: LYASE
Organism(s): Pantoea agglomerans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-11-16 Released: 2012-02-22
Deposition Author(s): Geiger, J., Strom, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.247
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Insights into the mechanistic pathway of the Pantoea agglomerans phenylalanine aminomutase.

Strom, S., Wanninayake, U., Ratnayake, N.D., Walker, K.D., Geiger, J.H.

(2012) Angew Chem Int Ed Engl 51: 2898-2902

PubMed: 22319000 Search on PubMed
DOI: https://doi.org/10.1002/anie.201108525
Primary Citation of Related Structures:
3UNV

Organizational Affiliation

Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.

Macromolecule Content

Total Structure Weight: 122.3 kDa
Atom Count: 8,538
Modelled Residue Count: 1,028
Deposited Residue Count: 1,094
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AdmH	A, B	547	Pantoea agglomerans	Mutation(s): 0
UniProt
Find proteins for Q84FL5 (Enterobacter agglomerans) Explore Q84FL5 Go to UniProtKB: Q84FL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q84FL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHE Query on PHE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SFE Query on SFE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B]	C [auth A], M [auth B]	(3S)-3-amino-3-phenylpropanoic acid C₉ H₁₁ N O₂ UJOYFRCOTPUKAK-QMMMGPOBSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	E [auth A], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] L [auth B] F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KWS Query on KWS	A, B	L-PEPTIDE LINKING	C₉ H₁₃ N₃ O₄		THR, SER, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.247
R-Value Work: 0.204
R-Value Observed: 0.206
Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.964	α = 90
b = 185.844	β = 90
c = 72.56	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

Geiger, J.

Strom, S.

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2012-11-14
Changes: Database references
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations