2P17 | pdb_00002p17

Crystal structure of GK1651 from Geobacillus kaustophilus

PDB DOI: https://doi.org/10.2210/pdb2P17/pdb

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

Deposited: 2007-03-02 Released: 2007-05-01
Deposition Author(s): Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.213 (Depositor), 0.212 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of GK1651 from Geobacillus kaustophilus

Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 31.52 kDa
Atom Count: 2,163
Modeled Residue Count: 249
Deposited Residue Count: 277
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin-like protein	A	277	Geobacillus kaustophilus HTA426	Mutation(s): 9 Gene Names: GK1651
UniProt
Find proteins for Q5KZF0 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KZF0 Go to UniProtKB: Q5KZF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5KZF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.52 Å
R-Value Free: 0.213 (Depositor), 0.212 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.571	α = 90
b = 59.823	β = 90
c = 69.685	γ = 90

Software Package:

Software Name	Purpose
SGXPRO	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SGXPRO	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-09-13
Changes: Advisory, Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-11-20
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary