2RHM | pdb_00002rhm

Crystal structure of a putative kinase (caur_3907) from chloroflexus aurantiacus j-10-fl at 1.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb2RHM/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Chloroflexus aurantiacus J-10-fl
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-09 Released: 2007-11-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.181 (Depositor), 0.189 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative kinase (ZP_00765535.1) from Chloroflexus aurantiacus J-10-fl at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 86.72 kDa
Atom Count: 6,378
Modeled Residue Count: 745
Deposited Residue Count: 772
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative kinase	A, B, C, D	193	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Gene Names: ZP_00765535.1, CaurDRAFT_1197
UniProt
Find proteins for A9WDG5 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDG5 Go to UniProtKB: A9WDG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9WDG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D]	G [auth B], K [auth D]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	H [auth B], L [auth D], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain L [auth D] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	E [auth A], F [auth B], I [auth C], J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [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: 1.70 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.181 (Depositor), 0.189 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.93	α = 90
b = 76.79	β = 90
c = 129.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Structure summary

2RHM | pdb_00002rhm

Crystal structure of a putative kinase (caur_3907) from chloroflexus aurantiacus j-10-fl at 1.70 A resolution

Literature

Crystal structure of putative kinase (ZP_00765535.1) from Chloroflexus aurantiacus J-10-fl at 1.70 A resolution

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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