8CU5 | pdb_00008cu5

Crystal Structure of Putative Cyclophilin B from Brugia malayi

PDB DOI: https://doi.org/10.2210/pdb8CU5/pdb

Classification: ISOMERASE
Organism(s): Brugia malayi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-16 Released: 2022-05-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Putative Cyclophilin B from Brugia malayi

DeBouver, N.D., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 65.29 kDa
Atom Count: 4,840
Modeled Residue Count: 549
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A, B, C	194	Brugia malayi	Mutation(s): 0 Gene Names: SM7 EC: 5.2.1.8
UniProt
Find proteins for A0A0R3QSA7 (Brugia timori) Explore A0A0R3QSA7 Go to UniProtKB: A0A0R3QSA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R3QSA7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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 M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth C]	G [auth A], H [auth B], J [auth C], M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	D [auth A] E [auth A] F [auth A] I [auth B] K [auth C] D [auth A], E [auth A], F [auth A], I [auth B], K [auth C], L [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.22	α = 90
b = 137.22	β = 90
c = 143.26	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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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.