2HR2 | pdb_00002hr2

Crystal structure of a tpr-like protein (ct2138) from chlorobium tepidum tls at 2.54 A resolution

PDB DOI: https://doi.org/10.2210/pdb2HR2/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Chlorobaculum tepidum TLS
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-07-19 Released: 2006-09-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.232 (Depositor), 0.240 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein (NP_663012.1) from Chlorobium tepidum TLS at 2.54 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 107.88 kDa
Atom Count: 7,235
Modeled Residue Count: 940
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D, E A, B, C, D, E, F	159	Chlorobaculum tepidum TLS	Mutation(s): 7 Gene Names: NP_663012.1
UniProt
Find proteins for Q8KAL8 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KAL8 Go to UniProtKB: Q8KAL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KAL8
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.232 (Depositor), 0.240 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32HR2

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.09	α = 90
b = 91.28	β = 90
c = 176.17	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHARP	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-09-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-09-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary