4DIM | pdb_00004dim

Crystal structure of phosphoribosylglycinamide synthetase from Anaerococcus prevotii

PDB DOI: https://doi.org/10.2210/pdb4DIM/pdb

Classification: LIGASE
Organism(s): Anaerococcus prevotii DSM 20548
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-31 Released: 2012-02-29
Deposition Author(s): Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.228 (Depositor), 0.224 (DCC)
R-Value Work:
0.184 (Depositor), 0.194 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of phosphoribosylglycinamide synthetase from Anaerococcus prevotii

Michalska, K., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 45.8 kDa
Atom Count: 3,093
Modeled Residue Count: 393
Deposited Residue Count: 403
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylglycinamide synthetase	A	403	Anaerococcus prevotii DSM 20548	Mutation(s): 0 Gene Names: Apre_1268
UniProt
Find proteins for C7RDM8 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / NCTC 11806 / PC1)) Explore C7RDM8 Go to UniProtKB: C7RDM8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7RDM8
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.228 (Depositor), 0.224 (DCC)
R-Value Work: 0.184 (Depositor), 0.194 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.27	α = 90
b = 84.467	β = 100.54
c = 49.642	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
SHELX	model building
ABS	model building
HELICAP	model building
BUCCANEER	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.