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- PDB-3uch: Crystal structure of a peptidyl-prolyl cis-trans isomerase E (PPI... -

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Basic information

Entry
Database: PDB / ID: 3uch
TitleCrystal structure of a peptidyl-prolyl cis-trans isomerase E (PPIE) from Homo sapiens at 2.50 A resolution
ComponentsPeptidyl-prolyl cis-trans isomerase E
KeywordsISOMERASE / Cyclophilin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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 / protein peptidyl-prolyl isomerization / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA splicing, via spliceosome / 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 / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a Hypotherical Peptidyl-prolyl cis-trans isomerase E (PPIE) from Homo sapiens at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Structure summary
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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 E


Theoretical massNumber of molelcules
Total (without water)19,3191
Polymers19,3191
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase E

A: Peptidyl-prolyl cis-trans isomerase E

A: Peptidyl-prolyl cis-trans isomerase E


Theoretical massNumber of molelcules
Total (without water)57,9583
Polymers57,9583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area3890 Å2
ΔGint-14 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.232, 116.232, 116.232
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRPAHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE PROTEIN HAS ASSOCIATED INTO TRIMERS THAT ARE PREDICTED TO BE STABLE.

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Components

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


Mass: 19319.230 Da / Num. of mol.: 1 / Fragment: residues 129-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC008451, CYP33, PPIE / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 129-301 OF THE TARGET SEQUENCE. THE SEQUENCE NUMBERING CORRESPONDS TO ISOFORM A (UNIPROTKB ID Q9UNP9-1)

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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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20.0% PEG-1000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97894
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.5→29.058 Å / Num. all: 9184 / Num. obs: 9184 / % possible obs: 99.9 % / Redundancy: 23.2 % / Rsym value: 0.149 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.57120.8012.771195930.801100
2.57-2.6423.71.1684.3152926461.168100
2.64-2.7124.21.0245.1158696551.024100
2.71-2.824.40.6776.5151576220.677100
2.8-2.8924.30.4549147746080.454100
2.89-2.9924.20.34510.8143025900.345100
2.99-3.124.20.28412.8134585550.284100
3.1-3.2324.30.22116.3132035430.221100
3.23-3.3724.20.18819.8127105260.188100
3.37-3.5424.10.15122.2120084990.151100
3.54-3.7324.20.13324.6116244810.133100
3.73-3.9523.90.11426.1109204570.114100
3.95-4.23240.11327.9102604280.113100
4.23-4.5723.90.0993195403990.099100
4.57-523.60.11631.387933730.116100
5-5.5923.60.1243078583330.124100
5.59-6.4623.30.11429.769042960.114100
6.46-7.91230.10530.760402630.105100
7.91-11.1822.50.08834.545772030.088100
11.18-29.05820.20.08931.423031140.08994.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.058 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.617 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 437 4.8 %RANDOM
Rwork0.1901 ---
obs0.1912 9184 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 110.33 Å2 / Biso mean: 59.869 Å2 / Biso min: 38.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 0 49 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221361
X-RAY DIFFRACTIONr_bond_other_d0.0010.02948
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9511831
X-RAY DIFFRACTIONr_angle_other_deg0.86432316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5724.92163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07515238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.347156
X-RAY DIFFRACTIONr_chiral_restr0.090.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_mcbond_it0.6511.5854
X-RAY DIFFRACTIONr_mcbond_other0.1181.5360
X-RAY DIFFRACTIONr_mcangle_it1.25621368
X-RAY DIFFRACTIONr_scbond_it1.9463507
X-RAY DIFFRACTIONr_scangle_it3.2134.5462
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 31 -
Rwork0.281 649 -
all-680 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 49.585 Å / Origin y: 46.026 Å / Origin z: 17.437 Å
111213212223313233
T0.2353 Å20.1036 Å2-0.0535 Å2-0.1617 Å20.022 Å2--0.3707 Å2
L2.5346 °20.5213 °20.5308 °2-2.9722 °2-0.3649 °2--2.0849 °2
S0.1602 Å °0.3125 Å °-0.2949 Å °-0.2731 Å °-0.0794 Å °0.1046 Å °0.4224 Å °0.3861 Å °-0.0808 Å °

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