1W8I | pdb_00001w8i

The Structure of gene product af1683 from Archaeoglobus fulgidus.

PDB DOI: https://doi.org/10.2210/pdb1W8I/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-09-22 Released: 2004-11-16
Deposition Author(s): Midwest Center for Structural Genomics (MCSG), Cuff, M.E., Zhang, R., Ginell, S.L., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.225 (Depositor), 0.202 (DCC)
R-Value Work:
0.211 (Depositor), 0.203 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

The Structure of Gene Product Af1683 from Archaeoglobus Fulgidus

Cuff, M.E., Zhang, R., Ginell, S.L., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 17.96 kDa
Atom Count: 1,399
Modeled Residue Count: 155
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE VAPC RIBONUCLEASE AF_1683	A	156	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 EC: 3.1
UniProt
Find proteins for O28590 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28590 Go to UniProtKB: O28590
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O28590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225 (Depositor), 0.202 (DCC)
R-Value Work: 0.211 (Depositor), 0.203 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.73	α = 90
b = 66.73	β = 90
c = 181.381	γ = 120

Software Package:

Software Name	Purpose
DM	model building
HKL-2000	data reduction
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
ARP/wARP	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-11-16

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2004-11-16
Type: Initial release
Version 1.1: 2012-02-22
Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2017-05-24
Changes: Database references
Version 1.3: 2017-06-28
Changes: Refinement description
Version 1.4: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, 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.