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- PDB-9c5d: E. coli peptidyl-prolyl cis-trans isomerase containing (2S,3S)-4-... -

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Basic information

Entry
Database: PDB / ID: 9c5d
TitleE. coli peptidyl-prolyl cis-trans isomerase containing (2S,3S)-4-Fluorovaline
ComponentsPeptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / Peptidyl-prolyl cis-trans isomerase / Non-canonical amino acids / fluorinated valine
Function / homology
Function and homology information


chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytosol
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / 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
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFrkic, R.L. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: Biochemistry / Year: 2024
Title: 1.3 angstrom Crystal Structure of E. coli Peptidyl-Prolyl Isomerase B with Uniform Substitution of Valine by (2 S ,3 S )-4-Fluorovaline Reveals Structure Conservation and Multiple Staggered ...Title: 1.3 angstrom Crystal Structure of E. coli Peptidyl-Prolyl Isomerase B with Uniform Substitution of Valine by (2 S ,3 S )-4-Fluorovaline Reveals Structure Conservation and Multiple Staggered Rotamers of CH 2 F Groups.
Authors: Frkic, R.L. / Tan, Y.J. / Maleckis, A. / Chilton, N.F. / Otting, G. / Jackson, C.J.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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 B
B: Peptidyl-prolyl cis-trans isomerase B
C: Peptidyl-prolyl cis-trans isomerase B
D: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,49512
Polymers77,1654
Non-polymers1,3318
Water17,096949
1
A: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


  • defined by author
  • 19.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,5923
Polymers19,2911
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


  • defined by author
  • 19.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,5003
Polymers19,2911
Non-polymers2092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


  • defined by author
  • 19.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,6544
Polymers19,2911
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


  • defined by author
  • 19.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,7502
Polymers19,2911
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.623, 84.005, 123.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peptidyl-prolyl cis-trans isomerase B / PPIase B / Rotamase B


Mass: 19291.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ppiB, b0525, JW0514 / Production host: Escherichia coli (E. coli) / References: UniProt: P23869, peptidylprolyl isomerase

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Non-polymers , 7 types, 957 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H42O11 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 31 % (w/v) PEG 3350, 0.1 M Tris pH 7.0, 0.2 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→42.18 Å / Num. obs: 203025 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.018 / Rrim(I) all: 0.067 / Χ2: 1.02 / Net I/σ(I): 18.1 / Num. measured all: 2724991
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 2.107 / Num. measured all: 127100 / Num. unique obs: 9926 / CC1/2: 0.514 / Rpim(I) all: 0.61 / Rrim(I) all: 2.194 / Χ2: 1.05 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→42.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 10356 5.1 %
Rwork0.1643 --
obs0.1654 202907 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 89 949 6298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.032
X-RAY DIFFRACTIONf_dihedral_angle_d9.911810
X-RAY DIFFRACTIONf_chiral_restr0.085834
X-RAY DIFFRACTIONf_plane_restr0.006998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.28293220.26176379X-RAY DIFFRACTION100
1.31-1.330.26553500.25076345X-RAY DIFFRACTION100
1.33-1.350.27953500.23636343X-RAY DIFFRACTION100
1.35-1.360.23883580.22236318X-RAY DIFFRACTION100
1.36-1.380.2683140.23266402X-RAY DIFFRACTION100
1.38-1.40.26883220.2376398X-RAY DIFFRACTION100
1.4-1.420.25753280.20866390X-RAY DIFFRACTION100
1.42-1.440.24913410.20056333X-RAY DIFFRACTION100
1.44-1.460.23693660.17916375X-RAY DIFFRACTION100
1.46-1.490.21183290.17146366X-RAY DIFFRACTION100
1.49-1.510.21723300.16146386X-RAY DIFFRACTION100
1.51-1.540.18153310.156385X-RAY DIFFRACTION100
1.54-1.570.18223410.14866378X-RAY DIFFRACTION100
1.57-1.60.17673230.14786407X-RAY DIFFRACTION100
1.6-1.640.18493740.14826350X-RAY DIFFRACTION100
1.64-1.680.19623580.15186396X-RAY DIFFRACTION100
1.68-1.720.17533960.1516341X-RAY DIFFRACTION100
1.72-1.760.20633150.16576414X-RAY DIFFRACTION100
1.76-1.820.193410.15816433X-RAY DIFFRACTION100
1.82-1.870.18353710.15136374X-RAY DIFFRACTION100
1.87-1.940.16793470.15066414X-RAY DIFFRACTION100
1.94-2.020.16223800.15216391X-RAY DIFFRACTION100
2.02-2.110.16713580.16096408X-RAY DIFFRACTION100
2.11-2.220.17813240.15316487X-RAY DIFFRACTION100
2.22-2.360.1843590.15586419X-RAY DIFFRACTION100
2.36-2.540.19083340.16716497X-RAY DIFFRACTION100
2.54-2.80.18253590.17256469X-RAY DIFFRACTION100
2.8-3.210.19343170.17916576X-RAY DIFFRACTION100
3.21-4.040.17773770.15436545X-RAY DIFFRACTION100
4.04-42.180.17183410.15786832X-RAY DIFFRACTION100

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