1XRH | pdb_00001xrh

Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli

PDB DOI: https://doi.org/10.2210/pdb1XRH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-10-14 Released: 2004-10-26
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.250 (Depositor), 0.262 (DCC)
R-Value Work:
0.192 (Depositor), 0.206 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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This is version 1.7 of the entry. See complete history.

Literature

Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli

Rajashankar, K.R., Kniewel, R., Lima, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 309.59 kDa
Atom Count: 21,480
Modeled Residue Count: 2,734
Deposited Residue Count: 2,808
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ureidoglycolate Dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	351	Escherichia coli	Mutation(s): 12 Gene Names: ALLD EC: 1.1.1.154 (PDB Primary Data), 1.1.1.350 (UniProt)
UniProt
Find proteins for P77555 (Escherichia coli (strain K12)) Explore P77555 Go to UniProtKB: P77555
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77555
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.250 (Depositor), 0.262 (DCC)
R-Value Work: 0.192 (Depositor), 0.206 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.715	α = 90
b = 129.916	β = 95.77
c = 106.468	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
BEAST	model building
SHARP	phasing
RESOLVE	model building
CNS	refinement
BEAST	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-10-26

Deposition Author(s):

Rajashankar, K.R.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-10-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-10-03
Changes: Data collection, Refinement description
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Refinement description
Version 1.6: 2023-11-15
Changes: Data collection
Version 1.7: 2024-11-13
Changes: 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.