1YNB | pdb_00001ynb

crystal structure of genomics APC5600

PDB DOI: https://doi.org/10.2210/pdb1YNB/pdb

Classification: HYDROLASE
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-01-24 Released: 2005-03-08
Deposition Author(s): Dong, A., Skarina, T., Savchenko, A., Pai, E.F., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.243 (Depositor), 0.242 (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 1YNB

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

Literature

Crystal structure of genomics AF1432 by Sulfur SAD methods

Dong, A., Skarina, T., Savchenko, A., Pai, E.F., Edwards, A.

To be published.

Macromolecule Content

Total Structure Weight: 59.54 kDa
Atom Count: 4,303
Modeled Residue Count: 501
Deposited Residue Count: 519
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein AF1432	A, B, C	173	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF1432 EC: 3.1.3.89
UniProt
Find proteins for O28840 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28840 Go to UniProtKB: O28840
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O28840
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.243 (Depositor), 0.242 (DCC)
R-Value Work: 0.206 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.32	α = 90
b = 131.41	β = 117.2
c = 58.56	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-03-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2011-10-05
Changes: Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references

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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.