3HID | pdb_00003hid

Crystal structure of adenylosuccinate synthetase from Yersinia pestis CO92

PDB DOI: https://doi.org/10.2210/pdb3HID/pdb

Classification: LIGASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-19 Released: 2009-06-02
Deposition Author(s): Zhang, R., Zhou, M., Peterson, S., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.198 (Depositor), 0.205 (DCC)
R-Value Work:
0.160 (Depositor), 0.173 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the adenylosuccinate synthetase from Yersinia pestis CO92

Zhang, R., Zhou, M., Peterson, S., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 47.6 kDa
Atom Count: 3,938
Modeled Residue Count: 424
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	A	432	Yersinia pestis CO92	Mutation(s): 0 Gene Names: gi:16120713, purA, y0635, YPO0378, YP_0534 EC: 6.3.4.4
UniProt
Find proteins for Q8ZIV7 (Yersinia pestis) Explore Q8ZIV7 Go to UniProtKB: Q8ZIV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZIV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198 (Depositor), 0.205 (DCC)
R-Value Work: 0.160 (Depositor), 0.173 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.903	α = 90
b = 68.903	β = 90
c = 199.166	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.