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- PDB-3ui5: Crystal structure of human Parvulin 14 -

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Basic information

Entry
Database: PDB / ID: 3ui5
TitleCrystal structure of human Parvulin 14
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 4
KeywordsISOMERASE / peptidyl-prolyl-isomerase
Function / homology
Function and homology information


preribosome / bent DNA binding / localization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spindle / rRNA processing / chromosome / double-stranded DNA binding / mitochondrial matrix ...preribosome / bent DNA binding / localization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spindle / rRNA processing / chromosome / double-stranded DNA binding / mitochondrial matrix / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase PIN4 / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsMueller, J.W. / Link, N.M. / Matena, A. / Hoppstock, L. / Rueppel, A. / Bayer, P. / Blankenfeldt, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Crystallographic proof for an extended hydrogen-bonding network in small prolyl isomerases.
Authors: Mueller, J.W. / Link, N.M. / Matena, A. / Hoppstock, L. / Ruppel, A. / Bayer, P. / Blankenfeldt, W.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Structure summary
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7448
Polymers11,1611
Non-polymers5827
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.170, 47.060, 51.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 / Parvulin-14 / Par14 / hPar14 / Parvulin-17 / Par17 / hPar17 / Peptidyl-prolyl cis-trans isomerase ...Parvulin-14 / Par14 / hPar14 / Parvulin-17 / Par17 / hPar17 / Peptidyl-prolyl cis-trans isomerase Pin4 / PPIase Pin4 / Peptidyl-prolyl cis/trans isomerase EPVH / hEPVH / Rotamase Pin4


Mass: 11161.042 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN4, Q9Y237 / Plasmid: pET-41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y237, peptidylprolyl isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1.88 Å3/Da / Density % sol: 34.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris, 2.5 M (NH4)2SO4, 3-20 mM Ala-Pro, pH 8.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 940887 / Rmerge(I) obs: 0.051 / D res high: 1.4 Å / Num. obs: 31317 / % possible obs: 98.5
ReflectionResolution: 1.4→34.84 Å / Num. obs: 16763 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.047 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 82.35
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.50.149.661382892926193.8
1.5-1.60.07760.2912957023921100
1.6-1.70.06469.2910393118801100
1.7-1.80.05778.018329314911100
1.8-1.90.05584.17653731158197.4
1.9-20.05391.0153678968198.9
2-2.50.04699.591581652816198.7
2.5-30.047109.917428112771100
3-40.052126.1772751038199.3
4-50.047137.4627436384199.7
5-100.046126.67257673721100
10-200.041125.273015541100
20-300.04966.951306175
30-34.841.1053211100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0077refinement
PDB_EXTRACT3.1data extraction
RefinementResolution: 1.4→34.84 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.573 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 821 4.9 %RANDOM
Rwork0.0962 15942 --
obs0.0983 16763 98.48 %-
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 max: 56.35 Å2 / Biso mean: 10.2658 Å2 / Biso min: 2.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 0 30 166 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02855
X-RAY DIFFRACTIONr_bond_other_d0.0080.02613
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.9981151
X-RAY DIFFRACTIONr_angle_other_deg1.1663.0011492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0492435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91215162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.091155
X-RAY DIFFRACTIONr_chiral_restr0.4030.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021921
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02164
X-RAY DIFFRACTIONr_rigid_bond_restr4.50631468
X-RAY DIFFRACTIONr_sphericity_free36.326521
X-RAY DIFFRACTIONr_sphericity_bonded9.37751597
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 47 -
Rwork0.222 912 -
all-959 -
obs--85.78 %

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