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- PDB-2gw2: Crystal structure of the peptidyl-prolyl isomerase domain of huma... -

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Basic information

Entry
Database: PDB / ID: 2gw2
TitleCrystal structure of the peptidyl-prolyl isomerase domain of human cyclophilin G
ComponentsPeptidyl-prolyl cis-trans isomerase G
KeywordsISOMERASE / mutation / surface mutagenesis / mutant / ppiase / cis-trans isomerization / peptidyl-prolyl isomerase / protein folding / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cyclosporin A binding / protein peptidyl-prolyl isomerization / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear matrix / SARS-CoV-1 activates/modulates innate immune responses / protein folding / nuclear speck ...cyclosporin A binding / protein peptidyl-prolyl isomerization / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear matrix / SARS-CoV-1 activates/modulates innate immune responses / protein folding / nuclear speck / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 G
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBernstein, G. / Tempel, W. / Davis, T. / Newman, E.M. / Finerty Jr., P.J. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Bernstein, G. / Tempel, W. / Davis, T. / Newman, E.M. / Finerty Jr., P.J. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: PLoS Biol. / Year: 2010
Title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
Authors: Davis, T.L. / Walker, J.R. / Campagna-Slater, V. / Finerty, P.J. / Paramanathan, R. / Bernstein, G. / MacKenzie, F. / Tempel, W. / Ouyang, H. / Lee, W.H. / Eisenmesser, E.Z. / Dhe-Paganon, S.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase G


Theoretical massNumber of molelcules
Total (without water)21,8435
Polymers21,8431
Non-polymers04
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.432, 65.504, 69.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase G / Peptidyl-prolyl isomerase G / PPIase G / Rotamase G / Cyclophilin G / Clk-associating RS- ...Peptidyl-prolyl isomerase G / PPIase G / Rotamase G / Cyclophilin G / Clk-associating RS-cyclophilin / CARS-cyclophilin / CARS-Cyp / SR-cyclophilin / SRcyp / SR-cyp / CASP10


Mass: 21842.746 Da / Num. of mol.: 1 / Fragment: residues 1-179 / Mutation: K106A, E107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIG / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus RIL / References: UniProt: Q13427, peptidylprolyl isomerase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 14841 / % possible obs: 90 % / Redundancy: 4 % / Rmerge(I) obs: 0.148 / Χ2: 1.66 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.8-1.8656.42.20.639080.854
1.86-1.9471.82.70.51411440.996
1.94-2.0390.63.50.4414781.063
2.03-2.1397.14.30.38815781.235
2.13-2.2797.74.30.26715841.6
2.27-2.4498.54.30.29716161.497
2.44-2.6998.44.40.21516201.528
2.69-3.0898.44.40.15416221.807
3.08-3.8896.74.40.09816242.549
3.88-3092.94.40.0716672.153

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1A58

1a58


Resolution: 1.8→29.617 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.189 / SU B: 4.199 / SU ML: 0.129 / ESU R: 0.175 / ESU R Free: 0.172
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/WARP, Molprobity were also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 728 4.985 %Random
Rwork0.2168 ---
all0.22 ---
obs-14604 89.136 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.093 Å20 Å20 Å2
2---0.175 Å20 Å2
3----0.917 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 4 103 1449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221374
X-RAY DIFFRACTIONr_bond_other_d0.0020.02958
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9411851
X-RAY DIFFRACTIONr_angle_other_deg0.98132327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5524.24266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44315230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.908157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined0.180.2258
X-RAY DIFFRACTIONr_nbd_other0.1960.21060
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2659
X-RAY DIFFRACTIONr_nbtor_other0.0830.2673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it2.83621103
X-RAY DIFFRACTIONr_mcbond_other0.9282356
X-RAY DIFFRACTIONr_mcangle_it3.26431380
X-RAY DIFFRACTIONr_scbond_it2.9392592
X-RAY DIFFRACTIONr_scangle_it3.5923470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.8-1.8470.418390.3736060.376115955.651
1.847-1.8970.48340.3787080.383115664.187
1.897-1.9520.36340.3028550.304112279.234
1.952-2.0120.288580.2449380.247109091.376
2.012-2.0770.247500.2139960.214108196.762
2.077-2.150.262490.2099360.212101297.332
2.15-2.230.285470.2678760.268101391.116
2.23-2.3210.426510.3158130.32197188.98
2.321-2.4240.254530.1938340.19690697.903
2.424-2.5410.28460.1958280.19988898.423
2.541-2.6770.306380.2058050.20985498.712
2.677-2.8380.247390.1917490.19479798.871
2.838-3.0320.265340.217080.21375598.278
3.032-3.2720.314290.1926640.19870897.881
3.272-3.580.192310.1836030.18465496.942
3.58-3.9960.213330.2045170.20559991.82
3.996-4.60.267220.1564930.1654295.018
4.6-5.60.27190.1884110.19145993.682
5.6-7.7820.293130.2323390.23438192.388
7.782-29.6170.26390.211970.21223786.92

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