2EJA | pdb_00002eja

Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb2EJA/pdb

Classification: LYASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-16 Released: 2008-03-18
Deposition Author(s): Bagautdinov, B., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.270 (Depositor), 0.218 (DCC)
R-Value Work:
0.205 (Depositor), 0.176 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus

Bagautdinov, B., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 77.52 kDa
Atom Count: 6,206
Modeled Residue Count: 673
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen decarboxylase	A, B	338	Aquifex aeolicus	Mutation(s): 0 EC: 4.1.1.37
UniProt
Find proteins for O66667 (Aquifex aeolicus (strain VF5)) Explore O66667 Go to UniProtKB: O66667
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66667
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.270 (Depositor), 0.218 (DCC)
R-Value Work: 0.205 (Depositor), 0.176 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.473	α = 90
b = 80.403	β = 90
c = 128.999	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-03-18

Deposition Author(s):

Bagautdinov, B.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-03-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, 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.