3K67 | pdb_00003k67

Crystal structure of protein af1124 from archaeoglobus fulgidus

PDB DOI: https://doi.org/10.2210/pdb3K67/pdb
Entry: 3K67 supersedes: 2B3N

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-08 Released: 2009-10-20
Deposition Author(s): Chang, C., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.166 (Depositor), 0.169 (DCC)
R-Value Work:
0.146 (Depositor), 0.155 (DCC)
R-Value Observed:
0.147 (Depositor)

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

Literature

Crystal Structure of Protein Af1124 from Archaeoglobus Fulgidus

Chang, C., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 35.36 kDa
Atom Count: 3,047
Modeled Residue Count: 312
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative dehydratase AF1124	A, B	159	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: AF_1124
UniProt
Find proteins for O29141 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29141 Go to UniProtKB: O29141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29141
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.166 (Depositor), 0.169 (DCC)
R-Value Work: 0.146 (Depositor), 0.155 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.973	α = 90
b = 55.32	β = 93.36
c = 69.121	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 2B3N

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
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.