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- PDB-2r99: Crystal structure of cyclophilin ABH-like domain of human peptidy... -

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Basic information

Entry
Database: PDB / ID: 2r99
TitleCrystal structure of cyclophilin ABH-like domain of human peptidylprolyl isomerase E isoform 1
ComponentsPeptidyl-prolyl cis-trans isomerase E
KeywordsISOMERASE / CIS-TRANS ISOMERIZATION / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / mRNA processing / mRNA splicing / Nucleus / RNA-binding / Rotamase / Spliceosome
Function / homology
Function and homology information


poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / positive regulation of viral genome replication / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / Transcription-Coupled Nucleotide Excision Repair (TC-NER) ...poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / positive regulation of viral genome replication / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein folding / secretory granule lumen / ficolin-1-rich granule lumen / nuclear speck / intracellular membrane-bounded organelle / mRNA binding / Neutrophil degranulation / regulation of DNA-templated transcription / RNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / 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 ...Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsWalker, J.R. / Davis, T. / Newman, E.M. / Mackenzie, F. / 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
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionSep 25, 2007ID: 1ZCX
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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 1.4Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,9861
Polymers18,9861
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.635, 66.635, 77.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Rotamase E / Cyclophilin E / Cyclophilin 33


Mass: 18985.666 Da / Num. of mol.: 1 / Fragment: Cyclophilin domain: Residues 131-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIE, CYP33 / Plasmid: pET28A-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 34% PEG 8000, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 12, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→40 Å / Num. obs: 22683 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.041 / Net I/σ(I): 34.34
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6.36 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BIT

2bit


Resolution: 1.61→33.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.734 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1157 5.1 %RANDOM
Rwork0.162 ---
obs0.164 21499 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.61→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 0 215 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9481735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4482560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07915228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.991155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02986
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.2598
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2898
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.5825
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59921290
X-RAY DIFFRACTIONr_scbond_it3.723518
X-RAY DIFFRACTIONr_scangle_it3.864.5445
X-RAY DIFFRACTIONr_rigid_bond_restr3.93431343
X-RAY DIFFRACTIONr_sphericity_free3.5293215
X-RAY DIFFRACTIONr_sphericity_bonded2.72831265
LS refinement shellResolution: 1.61→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 81 -
Rwork0.179 1254 -
obs--78.25 %

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