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- PDB-8vrg: E. coli peptidyl-prolyl cis-trans isomerase containing delta1-mon... -

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Basic information

Entry
Database: PDB / ID: 8vrg
TitleE. coli peptidyl-prolyl cis-trans isomerase containing delta1-monofluoro-leucines
ComponentsPeptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / Peptidyl-prolyl cis-trans isomerase / Non-canonical amino acids / fluorinated leucine
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
Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsFrkic, R.L. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
CitationJournal: Biochemistry / Year: 2024
Title: Conformational Preferences of the Non-Canonical Amino Acids (2 S ,4 S )-5-Fluoroleucine, (2 S ,4 R )-5-Fluoroleucine, and 5,5'-Difluoroleucine in a Protein.
Authors: Frkic, R.L. / Tan, Y.J. / Abdelkader, E.H. / Maleckis, A. / Tarcoveanu, E. / Nitsche, C. / Otting, G. / Jackson, C.J.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.691, 50.675, 40.767
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19093.283 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.71 Å3/Da / Density % sol: 28.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 36 % PEG 3350, 0.1 M Tris hydrochloride pH 8.0, 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 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.22→40.75 Å / Num. obs: 42115 / % possible obs: 98.8 % / Redundancy: 6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Rrim(I) all: 0.141 / Χ2: 0.52 / Net I/σ(I): 5.8 / Num. measured all: 254727
Reflection shellResolution: 1.22→1.24 Å / % possible obs: 78.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 1.114 / Num. measured all: 8179 / Num. unique obs: 1756 / CC1/2: 0.769 / Rpim(I) all: 0.559 / Rrim(I) all: 1.252 / Χ2: 0.14 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→40.75 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 2141 5.1 %
Rwork0.1621 --
obs0.1635 41975 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 221 1559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.049
X-RAY DIFFRACTIONf_dihedral_angle_d6.262197
X-RAY DIFFRACTIONf_chiral_restr0.085210
X-RAY DIFFRACTIONf_plane_restr0.009267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.240.29981320.28432184X-RAY DIFFRACTION82
1.24-1.270.2521620.24412666X-RAY DIFFRACTION100
1.27-1.310.22831210.23482678X-RAY DIFFRACTION100
1.31-1.350.25041400.21742679X-RAY DIFFRACTION100
1.35-1.390.21811580.20412683X-RAY DIFFRACTION100
1.39-1.440.21331360.20242651X-RAY DIFFRACTION100
1.44-1.50.22261600.18792678X-RAY DIFFRACTION100
1.5-1.570.20421550.17862678X-RAY DIFFRACTION100
1.57-1.650.22461360.17452694X-RAY DIFFRACTION100
1.65-1.750.17831410.17482686X-RAY DIFFRACTION100
1.75-1.890.17421640.16222647X-RAY DIFFRACTION100
1.89-2.080.20721480.15692679X-RAY DIFFRACTION100
2.08-2.380.17121520.14672699X-RAY DIFFRACTION100
2.38-30.16341140.15532739X-RAY DIFFRACTION100
3-40.750.17631220.13362793X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.81910.43831.1572.06690.69780.8725-0.00290.048-0.11650.1415-0.19540.3510.0653-0.74170.16150.10940.01390.010.2832-0.04450.2105-17.70232.2657-10.6603
21.3641-0.8063-0.0731.2515-0.04191.9548-0.00560.01040.07070.0344-0.02140.0648-0.152-0.36850.01180.090.0321-0.01760.1328-0.00980.1152-10.25748.0732-12.6677
31.0869-0.38130.11131.73280.52171.7881-0.0110.02770.05230.0187-0.06850.0106-0.2717-0.20850.01670.1080.0261-0.02020.0918-0.01020.114-6.67548.6188-8.6849
40.5311-0.00550.6414.01871.14853.19690.0083-0.0333-0.00680.22080.0039-0.23320.0011-0.0295-0.01640.08730.016-0.00190.0707-0.00040.1206-1.585.5569-1.8776
53.15070.6782-0.10872.61481.09542.2732-0.0360.1684-0.31860.0417-0.19040.34950.2862-0.40970.23010.1163-0.0184-0.01610.122-0.00220.1591-12.2213-5.447-11.6272
68.541-1.4416-2.15842.9893-1.60814.52210.11210.10380.2912-0.1807-0.2265-0.38810.0290.17590.09760.13990.05120.0160.1129-0.00920.15761.3321-0.4567-23.1226
75.58651.754-6.09261.2536-1.95236.84410.29280.27970.09580.1219-0.0590.0671-0.0718-0.1449-0.13540.12540.0206-0.03390.2549-0.01820.2089-24.81853.661-11.7268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 121 )
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 170 )

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