1ZX8 | pdb_00001zx8

CRYSTAL STRUCTURE OF an atypical cyclophilin (peptidylprolyl cis-trans isomerase) (TM1367) FROM THERMOTOGA MARITIMA AT 1.90 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1ZX8/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-06-07 Released: 2005-07-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.210 (Depositor), 0.220 (DCC)
R-Value Work:
0.166 (Depositor), 0.179 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZX8

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

Literature

Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.

Jin, K.K., Krishna, S.S., Schwarzenbacher, R., McMullan, D., Abdubek, P., Agarwalla, S., Ambing, E., Axelrod, H., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Feuerhelm, J., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Knuth, M.W., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Miller, M.D., Moy, K., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Quijano, K., Reyes, R., Rife, C., Stevens, R.C., Spraggon, G., van den Bedem, H., Velasquez, J., White, A., Wolf, G., Han, G.W., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2006) Proteins 63: 1112-1118

PubMed: 16544291 Search on PubMed
DOI: https://doi.org/10.1002/prot.20894
Primary Citation Related Structures:
1ZX8

Organizational Affiliation

The Joint Center for Structural Genomics, Menlo Park, California, USA.

Macromolecule Content

Total Structure Weight: 47.54 kDa
Atom Count: 3,268
Modeled Residue Count: 382
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1367	A, B, C	136	Thermotoga maritima	Mutation(s): 3 Gene Names: tm1367
UniProt
Find proteins for Q9X187 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X187 Go to UniProtKB: Q9X187
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X187
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.210 (Depositor), 0.220 (DCC)
R-Value Work: 0.166 (Depositor), 0.179 (DCC)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.083	α = 90
b = 132.875	β = 90
c = 41.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, Refinement description, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.