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- PDB-7n3j: E. coli peptidyl-prolyl cis-trans isomerase, mutant Phe27CF3-Tyr/... -

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Basic information

Entry
Database: PDB / ID: 7n3j
TitleE. coli peptidyl-prolyl cis-trans isomerase, mutant Phe27CF3-Tyr/Phe98CF3-Tyr
ComponentsPeptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / Peptidyl-prolyl cis-trans isomerase / Non-canonical amino acids / Trifluoromethyl-tyrosine
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-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: 2 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
DepositionJun 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 13, 2021Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 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 2.2Dec 1, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.3Dec 8, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase B
B: Peptidyl-prolyl cis-trans isomerase B


Theoretical massNumber of molelcules
Total (without water)38,3432
Polymers38,3432
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.138, 39.216, 103.715
Angle α, β, γ (deg.)90.000, 95.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 1 through 168)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 1 - 168 / Label seq-ID: 1 - 168

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 1 through 168)BB

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Components

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


Mass: 19171.328 Da / Num. of mol.: 2 / Mutation: F27CF3-Tyr, F98CF3-Tyr
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ppiB, b0525, JW0514 / Production host: Escherichia coli B (bacteria) / References: UniProt: P23869, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.81 Å3/Da / Density % sol: 31.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris (pH 7.5-8.0), 34% PEG 3350, 200mM 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: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→34.42 Å / Num. obs: 18550 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.131 / Rrim(I) all: 0.335 / Net I/σ(I): 3.9 / Num. measured all: 120749 / Scaling rejects: 740
Reflection shell

Diffraction-ID: 1 / Redundancy: 6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.052.988801213340.61.3273.2770.898.9
8.94-34.420.09713802310.9850.0430.10611.197.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUL

2nul


Resolution: 2→34.42 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 40.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 917 4.96 %
Rwork0.248 17577 -
obs0.2501 18494 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.15 Å2 / Biso mean: 59.7901 Å2 / Biso min: 20.46 Å2
Refinement stepCycle: final / Resolution: 2→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 0 20 2680
Biso mean---50.9 -
Num. residues----337
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1598X-RAY DIFFRACTION11.504TORSIONAL
12B1598X-RAY DIFFRACTION11.504TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.110.41431270.38952425255298
2.11-2.240.39141080.33982511261998
2.24-2.410.3476910.3162531262298
2.41-2.650.36011500.30342477262799
2.65-3.040.36131610.29542493265499
3.04-3.820.29091500.23962517266799
3.82-34.420.20371300.18542623275399
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)
10.9946-1.6810.79835.94051.66773.59360.36080.81350.2229-0.7728-0.483-0.7852-0.13160.74190.27450.40440.09120.0020.86490.11530.262217.54371.794310.4239
20.78681.00920.07521.7570.96551.7920.29170.90320.2338-0.6528-0.38060.4268-0.1588-0.1644-0.00570.55150.1989-0.14440.77170.08560.24326.27695.65418.9945
32.01270.2941.30273.10351.61873.36060.28050.9936-0.099-0.4049-0.480.52720.13250.1790.20140.32120.1312-0.04160.4463-0.05910.23855.3017-3.857813.6808
46.7758-1.67561.98131.464-0.92357.54350.83581.0631-1.0181-0.672-0.42080.52250.9299-0.3897-0.46380.38690.2021-0.22030.5092-0.15010.44470.0867-12.08319.457
53.8998-2.5292-1.19437.14223.58426.7429-0.1890.12090.18790.8259-0.0881-0.66720.0870.58240.17360.43210.0226-0.11620.28180.04020.134312.88422.794422.2748
66.1974-1.16531.01513.128-0.46212.3195-0.00580.55391.11960.1615-0.2597-0.34140.20670.37760.24420.39990.0308-0.03950.41210.05720.33659.871410.438515.1299
74.87880.74611.10912.7992-1.77113.79310.0899-0.4505-0.39070.6007-0.3599-1.1308-0.10531.19060.02850.4252-0.0391-0.15830.94440.04320.591430.8572-9.706135.8319
81.7292-0.8670.38480.4417-0.20090.0940.2106-1.0815-0.31361.0359-0.1595-0.44320.02140.8297-0.18530.8269-0.0268-0.34050.87770.09740.411223.0558-12.841240.896
92.3322-0.53750.10480.2071-0.50552.74710.124-1.0319-0.45291.0319-0.2024-0.1752-0.21540.29930.00691.06560.0397-0.30570.90490.16390.584118.9284-12.726746.889
101.5049-1.4673-0.99922.76751.05037.85080.1462-0.78310.07260.624-0.2626-0.3934-0.62210.28250.1360.6293-0.0737-0.12740.69720.01510.294517.9016-3.519638.9396
112.31610.33470.07940.21250.07070.06590.2029-0.44690.03610.12240.01180.06220.0457-0.22331.07011.25970.0353-0.67140.6407-0.20550.068413.12023.721544.715
124.00281.04082.91915.70581.16724.86450.05510.72860.2808-0.3984-0.928-0.5478-0.16341.25690.97590.75140.1099-0.11921.02970.15230.394126.6359-8.002229.7508
133.401-0.48810.22233.9699-0.77375.0120.6590.0946-1.0019-0.2985-0.5050.36690.5811-0.55470.0070.7163-0.0056-0.33550.3818-0.09220.578911.7888-19.857831.4048
142.2031.5875-0.79571.3606-1.01451.24580.44810.2968-0.60070.58980.39530.1806-0.1228-0.0251-0.7470.84430.0959-0.19350.84810.16390.673237.2125-10.249336.7526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )A1 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 74 )A34 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 108 )A75 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 121 )A109 - 121
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 138 )A122 - 138
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 168 )A139 - 168
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 20 )B1 - 20
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 52 )B21 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 74 )B53 - 74
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 108 )B75 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 121 )B109 - 121
12X-RAY DIFFRACTION12chain 'B' and (resid 122 through 136 )B122 - 136
13X-RAY DIFFRACTION13chain 'B' and (resid 137 through 156 )B137 - 156
14X-RAY DIFFRACTION14chain 'B' and (resid 157 through 169 )B157 - 169

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