2A1F | pdb_00002a1f

Crystal Structure of Uridylate kinase

PDB DOI: https://doi.org/10.2210/pdb2A1F/pdb

Classification: TRANSFERASE
Organism(s): Haemophilus influenzae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-06-20 Released: 2005-06-28
Deposition Author(s): Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.263 (Depositor), 0.265 (DCC)
R-Value Work:
0.210 (Depositor), 0.216 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Uridylate kinase

Gorman, J., Shapiro, L.

To be published.

Macromolecule Content

Total Structure Weight: 161.83 kDa
Atom Count: 11,567
Modeled Residue Count: 1,406
Deposited Residue Count: 1,482
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate kinase	A, B, C, D, E A, B, C, D, E, F	247	Haemophilus influenzae	Mutation(s): 0 Gene Names: pyrH, smbA EC: 2.7.4 (PDB Primary Data), 2.7.4.22 (UniProt)
UniProt
Find proteins for P43890 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43890 Go to UniProtKB: P43890
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43890
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.263 (Depositor), 0.265 (DCC)
R-Value Work: 0.210 (Depositor), 0.216 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.369	α = 94.85
b = 79.889	β = 96.68
c = 79.899	γ = 96.88

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-06-28

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2005-06-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description

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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.