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- PDB-2nul: PEPTIDYLPROLYL ISOMERASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 2nul
TitlePEPTIDYLPROLYL ISOMERASE FROM E. COLI
ComponentsPEPTIDYLPROLYL ISOMERASE
KeywordsISOMERASE / ROTAMASE
Function / homology
Function and homology information


: / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cytosol
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli 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, E. coli 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 B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEdwards, K.J. / Ollis, D.L.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of cytoplasmic Escherichia coli peptidyl-prolyl isomerase: evidence for decreased mobility of loops upon complexation.
Authors: Edwards, K.J. / Ollis, D.L. / Dixon, N.E.
History
DepositionNov 14, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Aug 9, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYLPROLYL ISOMERASE


Theoretical massNumber of molelcules
Total (without water)18,1741
Polymers18,1741
Non-polymers00
Water1,60389
1
A: PEPTIDYLPROLYL ISOMERASE

A: PEPTIDYLPROLYL ISOMERASE


Theoretical massNumber of molelcules
Total (without water)36,3492
Polymers36,3492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)44.700, 68.200, 102.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-243-

HOH

21A-243-

HOH

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Components

#1: Protein PEPTIDYLPROLYL ISOMERASE / PEPTIDYLPROLYL CIS-TRANS ISOMERASE / CYCLOPHILIN


Mass: 18174.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P23869, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.14 Å3/Da / Density % sol: 42 %
Crystal growpH: 8.5
Details: CRYSTALLIZED FROM 100 MM TRIS PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG 3.4K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
250 mMimidazole1drop
31 mMEDTA1drop
41 mMdithiothreitol1drop
5100 mMTris1reservoir
60.2 Msodium acetate1reservoir
730 %(w/v)PEG34001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 9966 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057
Reflection shellResolution: 2→2.5 Å / % possible all: 91.5
Reflection
*PLUS
Num. measured all: 31874

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LOP (COORDS RECEIVED FROM AUTHORS IN ADVANCE OF DEPOSITION)

1lop


Resolution: 2.1→6 Å / Isotropic thermal model: RESTRAINED
RfactorNum. reflection% reflection
Rwork0.16 --
obs0.16 8404 93.5 %
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.0254 Å20 Å20 Å2
2---7.5515 Å20 Å2
3----7.5515 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 89 1306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.003
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.778
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.232 754 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.172
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.778

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