1YQE | pdb_00001yqe

Crystal Structure of Conserved Protein of Unknown Function AF0625

PDB DOI: https://doi.org/10.2210/pdb1YQE/pdb

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

Deposited: 2005-02-01 Released: 2005-03-15
Deposition Author(s): Liu, Y., Skarina, T., Dong, A., Kudritskam, M., Savchenko, A., Pai, E.F., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.230 (Depositor), 0.229 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YQE

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Conserved Hypothetical Protein AF0625

Liu, Y., Skarina, T., Dong, A., Kudritskam, M., Savchenko, A., Pai, E.F., Edwards, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.15 kDa
Atom Count: 2,474
Modeled Residue Count: 282
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical UPF0204 protein AF0625	A	282	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: gi\|2649994 EC: 3.1.1.96
UniProt
Find proteins for O29630 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29630 Go to UniProtKB: O29630
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29630
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.230 (Depositor), 0.229 (DCC)
R-Value Work: 0.206 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.294	α = 90
b = 73.787	β = 90
c = 99.232	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-03-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-15
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: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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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.