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- PDB-7rfd: E. coli peptidyl-prolyl cis-trans isomerase, mutant Phe4Ala Phe27... -

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Basic information

Entry
Database: PDB / ID: 7rfd
TitleE. coli peptidyl-prolyl cis-trans isomerase, mutant Phe4Ala Phe27CF3-Phe/Phe98CF3-Phe
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Peptidyl-prolyl cis-trans isomerase / Non-canonical amino acids / Trifluoromethyl-phenylalanine
Function / homology
Function and homology information


DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
THAP / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile
Similarity search - Domain/homology
THAP domain-containing protein 11
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFrkic, R.L. / Otting, G. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL170100019 Australia
Australian Research Council (ARC)DP210100088 Australia
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Through-Space Scalar 19 F- 19 F Couplings between Fluorinated Noncanonical Amino Acids for the Detection of Specific Contacts in Proteins.
Authors: Orton, H.W. / Qianzhu, H. / Abdelkader, E.H. / Habel, E.I. / Tan, Y.J. / Frkic, R.L. / Jackson, C.J. / Huber, T. / Otting, G.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 1, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 8, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,0631
Polymers19,0631
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.891, 34.891, 210.047
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 19063.230 Da / Num. of mol.: 1 / Mutation: F4A, F27CF3-Phe, F98CF3-Phe
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ppiB, ppiA / Production host: Escherichia coli B (bacteria) / References: UniProt: J7QN08, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% PEG 3350, 0.1M Tris-HCl (pH 8.0), 0.2M Sodium Acetate

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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: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.549
11-K, -H, -L20.451
ReflectionResolution: 1.35→35.01 Å / Num. obs: 31687 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.06 / Rrim(I) all: 0.257 / Net I/σ(I): 13.1 / Num. measured all: 545282 / Scaling rejects: 160
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.35-1.379.43.8321454015390.4261.2534.0411.3100
7.39-35.0119.10.05541222160.9980.0130.05743.299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7N3J

7n3j


Resolution: 1.35→35.01 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.406 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.009 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.149 1632 5.2 %RANDOM
Rwork0.1218 ---
obs0.1232 29926 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.78 Å2 / Biso mean: 13.181 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å2-0 Å2
2---1.77 Å2-0 Å2
3---3.54 Å2
Refinement stepCycle: final / Resolution: 1.35→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 189 1526
Biso mean---24.29 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171249
X-RAY DIFFRACTIONr_angle_refined_deg2.1911.6371870
X-RAY DIFFRACTIONr_angle_other_deg1.591.5882876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39923.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07215225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.555156
X-RAY DIFFRACTIONr_chiral_restr0.1220.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 112 -
Rwork0.205 2198 -
all-2310 -
obs--99.83 %

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