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- PDB-5xb0: 1.6 A crystal structure of peptidyl-prolyl cis-trans isomerase PP... -

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Basic information

Entry
Database: PDB / ID: 5xb0
Title1.6 A crystal structure of peptidyl-prolyl cis-trans isomerase PPIase from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO DC3000)
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP / PPIase / PSPTO-PPIase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain superfamily / Domain amino terminal to FKBP-type peptidyl-prolyl isomerase / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological species[Pseudomonas syringae] pv. tomato str. DC3000 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, H. / Gao, Y. / Li, M. / Chang, W.
CitationJournal: To Be Published
Title: 1.6 A crystal structure of peptidyl-prolyl cis-trans isomerase PPIase from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO DC3000)
Authors: Zhang, H. / Gao, Y. / Li, M. / Chang, W.
History
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 19, 2017ID: 3OE2
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,4502
Polymers14,3001
Non-polymers1501
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-0 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.222, 44.099, 82.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 14300.126 Da / Num. of mol.: 1 / Fragment: UNP residues 91-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Pseudomonas syringae] pv. tomato str. DC3000 (bacteria)
Strain: DC3000 / Gene: PSPTO_0135 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q88B84, peptidylprolyl isomerase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.3 / Details: 0.4M pPotassium sodium tartrate / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→41.17 Å / Num. obs: 16027 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Χ2: 1.14 / Net I/σ(I): 49.24
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1182 / Rsym value: 0.254 / Χ2: 1.099 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FD9

1fd9


Resolution: 1.6→26.535 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.1975 1600 9.99 %
Rwork0.1681 --
obs0.1711 16024 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 10 172 1189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061048
X-RAY DIFFRACTIONf_angle_d1.0811428
X-RAY DIFFRACTIONf_dihedral_angle_d12.411389
X-RAY DIFFRACTIONf_chiral_restr0.044159
X-RAY DIFFRACTIONf_plane_restr0.005190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65160.25491070.2958X-RAY DIFFRACTION72
1.6516-1.71060.22651340.17671210X-RAY DIFFRACTION91
1.7106-1.77910.21291470.17171326X-RAY DIFFRACTION100
1.7791-1.86010.21861480.16651334X-RAY DIFFRACTION100
1.8601-1.95810.20411490.16941346X-RAY DIFFRACTION100
1.9581-2.08080.20341490.1621342X-RAY DIFFRACTION100
2.0808-2.24130.20071480.17881341X-RAY DIFFRACTION100
2.2413-2.46670.19931510.17841354X-RAY DIFFRACTION100
2.4667-2.82330.20121510.19121361X-RAY DIFFRACTION100
2.8233-3.55580.19111540.1661386X-RAY DIFFRACTION100
3.5558-26.53850.18331620.14961466X-RAY DIFFRACTION99

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