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- PDB-2ok3: X-ray structure of human cyclophilin J at 2.0 angstrom -

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Basic information

Entry
Database: PDB / ID: 2ok3
TitleX-ray structure of human cyclophilin J at 2.0 angstrom
ComponentsPeptidyl-prolyl cis-trans isomerase-like 3
KeywordsISOMERASE / beta-barrel / helix / disulfide bridge
Function / homology
Function and homology information


catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / mRNA splicing, via spliceosome / protein folding / nucleoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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 ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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
NICKEL (II) ION / Peptidyl-prolyl cis-trans isomerase-like 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsXia, Z.
CitationJournal: To be Published
Title: Targeting Cyclophilin J, a novel peptidyl-prolyl isomerase, can induce cellular G1/S arrest and repress the growth of Hepatocellular carcinoma
Authors: Chen, J. / Chen, S. / Huang, L. / Zhao, X. / Tan, J. / Huang, C. / Saiyin, H. / Zhang, M. / Zeng, X. / Xi, J. / Wan, B. / Zhao, Y. / Xia, Z. / Jiang, H. / Yi, Q. / Liu, J.O. / Yu, L.
History
DepositionJan 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2953
Polymers18,1781
Non-polymers1172
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.577, 40.577, 170.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase-like 3 / PPIase / Rotamase / Cyclophilin-like protein PPIL3 / Cyclophilin J / CyPJ


Mass: 18177.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Fetal Brain / Gene: PPIL3b / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9H2H8, peptidylprolyl isomerase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1mol/L Tris(pH=8.3), 0.01mol/L nickel(II)chloride hexahydrate, 17%(w/v) PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorDetector: IMAGE PLATE / Date: Oct 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 11824 / Num. obs: 11753 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.036
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.188 / Num. unique all: 1143 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1XYH

1xyh


Resolution: 2→22.11 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1335654.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1197 10.4 %RANDOM
Rwork0.202 ---
all0.207 11777 --
obs0.202 11519 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6417 Å2 / ksol: 0.313714 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å2-0.11 Å20 Å2
2--1.95 Å20 Å2
3----3.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→22.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 2 161 1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it0.81.5
X-RAY DIFFRACTIONc_mcangle_it1.312
X-RAY DIFFRACTIONc_scbond_it1.282
X-RAY DIFFRACTIONc_scangle_it1.982.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 138 12.6 %
Rwork0.222 954 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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