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- PDB-3bo7: Crystal structure of Toxoplasma gondii peptidyl-prolyl cis-trans ... -

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Basic information

Entry
Database: PDB / ID: 3bo7
TitleCrystal structure of Toxoplasma gondii peptidyl-prolyl cis-trans isomerase, 541.m00136
Components
  • CYCLOSPORIN ACiclosporin
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsWernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. ...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)
CitationJournal: To be Published
Title: Crystal Structure of Toxoplasma Gondii Peptidyl-Prolyl Cis-Trans Isomerase, 541.M00136.
Authors: 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.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
D: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
E: CYCLOSPORIN A
F: CYCLOSPORIN A
G: CYCLOSPORIN A
H: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,25737
Polymers97,7098
Non-polymers2,54829
Water8,719484
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
E: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9708
Polymers24,4272
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-56.2 kcal/mol
Surface area8850 Å2
MethodPISA
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
F: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8116
Polymers24,4272
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-41.7 kcal/mol
Surface area8870 Å2
MethodPISA
3
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
G: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,22411
Polymers24,4272
Non-polymers7979
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-76.2 kcal/mol
Surface area9330 Å2
MethodPISA
4
D: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE
H: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,25212
Polymers24,4272
Non-polymers82510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-72.7 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.631, 100.805, 86.184
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23D
33B
43C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVAL1AA160 - 166160 - 166
21PROPROVALVAL1BB160 - 166160 - 166
31PROPROVALVAL1CC160 - 166160 - 166
41PROPROVALVAL1DD160 - 166160 - 166
12GLYGLYPROPRO1AA60 - 6760 - 67
22GLYGLYPROPRO1BB60 - 6760 - 67
32GLYGLYPROPRO1CC60 - 6760 - 67
42GLYGLYPROPRO1DD60 - 6760 - 67
13GLUGLUASNASN2AA127 - 130127 - 130
23GLUGLUASNASN2DD127 - 130127 - 130
33GLUGLUASNASN2BB127 - 130127 - 130
43GLUGLUASNASN2CC127 - 130127 - 130

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYCLOPHILIN-TYPE / PPIASE / ROTAMASE


Mass: 23206.619 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Gene: 541.M00136 / Plasmid: P15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5A / References: UniProt: D0VWS5
#2: Protein/peptide
CYCLOSPORIN A / Ciclosporin / CICLOSPORIN / CICLOSPORINE / Ciclosporin


Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / Mass: 1220.625 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growpH: 7.3
Details: 28% PEG 3350, 0.2 M LISO4, 0.1 M HEPES PH 7.3, 2 MM TCEP, 2 MM CYCLOSPORIN A, 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 54466 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.083 / Net I/σ(I): 6.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.834 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.92 Å
Translation2.5 Å24.92 Å

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUO

2fuo


Resolution: 2.35→33.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.865 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2422 5.1 %RANDOM
Rwork0.19 ---
obs0.192 47813 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.07 Å2
2---0.31 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.35→33.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 138 484 6298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9998059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59623.525278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.687151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0881546
X-RAY DIFFRACTIONr_chiral_restr0.0790.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024498
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22716
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23967
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2517
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5051.53705
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87925790
X-RAY DIFFRACTIONr_scbond_it1.16632493
X-RAY DIFFRACTIONr_scangle_it1.9294.52259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A51tight positional0.020.05
12B51tight positional0.020.05
13C51tight positional0.020.05
14D51tight positional0.020.05
21A49tight positional0.030.05
22B49tight positional0.020.05
23C49tight positional0.040.05
24D49tight positional0.040.05
31A16tight positional0.020.05
32D16tight positional0.010.05
33B16tight positional0.020.05
34C16tight positional0.020.05
31A19medium positional0.540.5
32D19medium positional0.240.5
33B19medium positional0.20.5
34C19medium positional0.220.5
11A51tight thermal0.040.5
12B51tight thermal0.080.5
13C51tight thermal0.080.5
14D51tight thermal0.040.5
21A49tight thermal0.040.5
22B49tight thermal0.050.5
23C49tight thermal0.090.5
24D49tight thermal0.080.5
31A16tight thermal0.110.5
32D16tight thermal0.050.5
33B16tight thermal0.130.5
34C16tight thermal0.090.5
31A19medium thermal0.682
32D19medium thermal0.452
33B19medium thermal0.512
34C19medium thermal0.582
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 185 -
Rwork0.28 3333 -
obs--99.94 %

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