3BO7 | pdb_00003bo7

Crystal structure of Toxoplasma gondii peptidyl-prolyl cis-trans isomerase, 541.m00136

PDB DOI: https://doi.org/10.2210/pdb3BO7/pdb

Classification: ISOMERASE/IMMUNOSUPPRESSANT
Organism(s): Toxoplasma gondii, Tolypocladium inflatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-17 Released: 2008-02-19
Deposition Author(s): Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Xiao, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.245 (Depositor), 0.239 (DCC)
R-Value Work:
0.190 (Depositor), 0.187 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Toxoplasma Gondii Peptidyl-Prolyl Cis-Trans Isomerase, 541.M00136.

Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Xiao, T.

To be published.

Macromolecule Content

Total Structure Weight: 100.26 kDa
Atom Count: 6,363
Modeled Residue Count: 713
Deposited Residue Count: 848
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE	A, B, C, D	201	Toxoplasma gondii	Mutation(s): 0 Gene Names: 541.M00136 EC: 5.2.1.8
UniProt
Find proteins for D0VWS5 (Toxoplasma gondii) Explore D0VWS5 Go to UniProtKB: D0VWS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWS5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	E, F, G, H	11	Tolypocladium inflatum	Mutation(s): 0

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 AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth G] SDF format, chain N [auth A] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain Z [auth C]	GA [auth D] HA [auth D] IA [auth D] JA [auth D] KA [auth G] GA [auth D], HA [auth D], IA [auth D], JA [auth D], KA [auth G], N [auth A], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth G] Focus chain N [auth A] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth G] Focus chain N [auth A] Focus chain Z [auth C]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	E, F, G, H	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	E, F, G, H	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
DAL Query on DAL	E, F, G, H	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MLE Query on MLE	E, F, G, H	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	E, F, G, H	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	E, F, G, H	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142 Query on PRD_000142	E, F, G, H	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.245 (Depositor), 0.239 (DCC)
R-Value Work: 0.190 (Depositor), 0.187 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.631	α = 90
b = 100.805	β = 116.28
c = 86.184	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-06-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-07-27
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
Version 1.4: 2012-12-12
Changes: Other
Version 1.5: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description