3RQ1

Crystal Structure of Aminotransferase Class I and II from Veillonella parvula

PDB DOI: https://doi.org/10.2210/pdb3RQ1/pdb

Classification: TRANSFERASE
Organism(s): Veillonella parvula DSM 2008
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-27 Released: 2011-05-18
Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.263
R-Value Work: 0.190
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Aminotransferase Class I and II from Veillonella parvula

Kim, Y., Hatzos-Skintges, C., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 188.43 kDa
Atom Count: 13,495
Modelled Residue Count: 1,633
Deposited Residue Count: 1,672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class I and II	A, B, C, D	418	Veillonella parvula DSM 2008	Mutation(s): 0 Gene Names: Vpar_1105
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
OAA Query on OAA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C]	F [auth A], I [auth B], O [auth C]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain O [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	E [auth A] G [auth A] H [auth A] J [auth B] K [auth C] E [auth A], G [auth A], H [auth A], J [auth B], K [auth C], N [auth C], P [auth C], Q [auth D], R [auth D], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.263
R-Value Work: 0.190
R-Value Observed: 0.194
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M33RQ1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.991	α = 102.4
b = 81.057	β = 101.37
c = 106.395	γ = 102.95

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-05-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-05-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary