2QYH | pdb_00002qyh

Crystal structure of the hypothetical protein (gk1056) from geobacillus kaustophilus HTA426

PDB DOI: https://doi.org/10.2210/pdb2QYH/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Geobacillus kaustophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-08-15 Released: 2008-08-19
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Sekar, K., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the hypothetical protein (gk1056) from geobacillus kaustophilus HTA426

Jeyakanthan, J., Kanaujia, S.P., Sekar, K., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 121.07 kDa
Atom Count: 8,855
Modeled Residue Count: 1,027
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical conserved protein, GK1056	A, B, C, D	258	Geobacillus kaustophilus	Mutation(s): 0
UniProt
Find proteins for Q5L139 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L139 Go to UniProtKB: Q5L139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5L139
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.987	α = 90
b = 113.91	β = 90
c = 182.174	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-08-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-10-09
Changes: Structure summary