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- PDB-1xyh: Crystal Structure of Recombinant Human Cyclophilin J -

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Basic information

Entry
Database: PDB / ID: 1xyh
TitleCrystal Structure of Recombinant Human Cyclophilin J
Componentscyclophilin-like protein PPIL3b
KeywordsISOMERASE / cyclophilin J / beta-barrel / helix / disulfide bridge
Function / homology
Function and homology information


catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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
Peptidyl-prolyl cis-trans isomerase-like 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, L.-L. / Zhao, X.-M. / Huang, C.-Q. / Yu, L. / Xia, Z.-X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of recombinant human cyclophilin J, a novel member of the cyclophilin family.
Authors: Huang, L.L. / Zhao, X.M. / Huang, C.Q. / Yu, L. / Xia, Z.X.
History
DepositionNov 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: cyclophilin-like protein PPIL3b


Theoretical massNumber of molelcules
Total (without water)18,1781
Polymers18,1781
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.309, 41.309, 172.116
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 cyclophilin-like protein PPIL3b / Cyclophilin J


Mass: 18177.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIL3b / Organ: fetal brain / Plasmid: pTXB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H2H8, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Tris-HCl, PEG8000, DMSO, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: BRUKER / Detector: CCD / Date: Jun 26, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→27.51 Å / Num. all: 5798 / Num. obs: 5560 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.372 / Num. unique all: 499 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPL

2cpl


Resolution: 2.6→27.51 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 227854.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelyhood target using amplitude
RfactorNum. reflection% reflectionSelection details
Rfree0.236 567 10.6 %RANDOM
Rwork0.175 ---
all0.181 5333 --
obs0.175 5333 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4574 Å2 / ksol: 0.301138 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å25.07 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 0 26 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 51 11.5 %
Rwork0.248 391 -
obs-499 83.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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