2R5X

Crystal structure of uncharacterized conserved protein YugN from Geobacillus kaustophilus HTA426

PDB DOI: https://doi.org/10.2210/pdb2R5X/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Geobacillus kaustophilus HTA426
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-09-04 Released: 2007-09-11
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Shi, W., Toro, R., Meyer, A.J., Freeman, J., Wu, B., Koss, J., Groshong, C., Rodgers, L., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein YugN from Geobacillus kaustophilus HTA426.

Ramagopal, U.A., Patskovsky, Y., Shi, W., Toro, R., Meyer, A.J., Freeman, J., Wu, B., Koss, J., Groshong, C., Rodgers, L., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 30.3 kDa
Atom Count: 2,140
Modelled Residue Count: 233
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized conserved protein	A, B	129	Geobacillus kaustophilus HTA426	Mutation(s): 1 Gene Names: yugN, GK1089
UniProt
Find proteins for Q5L106 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L106 Go to UniProtKB: Q5L106
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5L106
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.158	α = 90
b = 92.319	β = 90
c = 33.843	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
SHELXE	model building
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Structure summary
Version 1.5: 2021-10-20
Changes: Database references
Version 1.6: 2024-02-21
Changes: Data collection

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.