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- PDB-8vrh: E. coli peptidyl-prolyl cis-trans isomerase containing delta2-mon... -

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Basic information

Entry
Database: PDB / ID: 8vrh
TitleE. coli peptidyl-prolyl cis-trans isomerase containing delta2-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


: / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Derived calculations / Category: citation / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
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
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)74,70716
Polymers73,1704
Non-polymers1,53812
Water6,521362
1
A: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6916
Polymers18,2921
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint8 kcal/mol
Surface area8440 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6994
Polymers18,2921
Non-polymers4063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint3 kcal/mol
Surface area7610 Å2
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8133
Polymers18,2921
Non-polymers5212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-1 kcal/mol
Surface area8020 Å2
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5053
Polymers18,2921
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint4 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.022, 83.003, 121.642
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: 18292.410 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 , 6 types, 374 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: 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: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 3350, 0.2M sodium acetate trihydrate, 0.1M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→24.53 Å / Num. obs: 73053 / % possible obs: 98.1 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.049 / Rrim(I) all: 0.103 / Χ2: 0.74 / Net I/σ(I): 8.5 / Num. measured all: 270092
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 98.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 1.103 / Num. measured all: 10853 / Num. unique obs: 4315 / CC1/2: 0.389 / Rpim(I) all: 0.814 / Rrim(I) all: 1.386 / Χ2: 0.54 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.43 Å / Cross valid method: THROUGHOUT / σ(F): 161.7 / Phase error: 26.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2474 3707 5.08 %
Rwork0.2078 --
obs0.2095 72953 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 102 362 5577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.182
X-RAY DIFFRACTIONf_dihedral_angle_d17.3571906
X-RAY DIFFRACTIONf_chiral_restr0.08777
X-RAY DIFFRACTIONf_plane_restr0.007949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.33741940.30063369X-RAY DIFFRACTION92
1.83-1.860.31941770.29113448X-RAY DIFFRACTION93
1.86-1.90.32351670.2853483X-RAY DIFFRACTION94
1.9-1.940.28522000.25693451X-RAY DIFFRACTION93
1.94-1.980.28751810.2563490X-RAY DIFFRACTION94
1.98-2.030.29611860.23743468X-RAY DIFFRACTION94
2.03-2.080.26861470.2233532X-RAY DIFFRACTION95
2.08-2.130.27581710.21893489X-RAY DIFFRACTION94
2.13-2.20.24581710.20853509X-RAY DIFFRACTION94
2.2-2.270.23841930.22423434X-RAY DIFFRACTION93
2.27-2.350.30031660.24093466X-RAY DIFFRACTION93
2.35-2.440.26771600.21363493X-RAY DIFFRACTION94
2.44-2.550.35511420.24083471X-RAY DIFFRACTION93
2.55-2.690.27321890.2133474X-RAY DIFFRACTION93
2.69-2.860.25531820.21613474X-RAY DIFFRACTION93
2.86-3.080.26341710.21873489X-RAY DIFFRACTION93
3.08-3.380.23921840.21473467X-RAY DIFFRACTION92
3.38-3.870.22412170.17693458X-RAY DIFFRACTION91
3.87-4.870.15241760.14923487X-RAY DIFFRACTION91
4.87-23.430.22061690.17713458X-RAY DIFFRACTION87
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)
14.9069-0.1959-1.47981.57190.0122.69820.0787-0.10720.0322-0.07040.14660.1534-0.077-0.2159-0.22170.18960.0164-0.01750.17620.04210.143318.239925.782420.5241
28.21970.12450.74373.0026-0.37031.44660.0710.40270.0073-0.35550.08560.2209-0.0923-0.2562-0.15230.22320.008-0.02470.18280.0180.108215.335922.187910.733
32.8145-0.13580.16341.8681-0.55912.3056-0.02840.0281-0.2596-0.16940.1251-0.02770.1086-0.1457-0.0880.1499-0.0098-0.00940.12320.01170.139523.225112.394117.0388
49.0547-6.9936-5.39049.60266.53734.5852-0.1731-0.52380.31040.28410.4623-0.2270.06130.1791-0.23880.17980.0064-0.00050.15690.01130.119423.120924.532322.9089
57.29142.36292.96773.6417-2.76286.54030.1244-0.9729-0.03540.6485-0.11620.2753-0.6376-0.39320.01420.23970.02960.03240.40420.05510.150215.57118.988631.8614
64.8539-0.945-2.35940.73182.46929.6857-0.0593-0.3109-0.9330.11180.07910.66370.9737-0.0357-0.01510.3424-0.0842-0.07390.36290.22380.49758.88194.695725.6108
73.83623.2647-1.45394.2591-3.6754.8017-0.25390.01990.3295-0.10490.55290.46520.0068-0.2418-0.26620.15290.0153-0.02670.27860.070.24089.855324.972519.1466
81.9658-0.8224-0.28444.82762.1314.43450.0396-0.1295-0.0475-0.03440.0691-0.02760.06470.3665-0.12270.12690.0004-0.01720.18540.02140.13026.683241.0959.7098
91.921-0.7241-0.46619.50240.47812.97520.1274-0.50080.17470.90550.0045-0.52780.12260.1531-0.14630.2031-0.0133-0.03760.2949-0.01370.14794.522742.235621.101
105.0618-1.39032.4872.36020.21834.04450.1584-0.117-0.23050.1315-0.12910.07840.3291-0.0144-0.02590.1542-0.0289-0.0010.16140.0290.1086-4.385934.100610.7634
113.30043.13974.05885.54754.58997.86580.3513-0.3755-0.18280.6554-0.2993-0.01471.105-0.7514-0.02960.3489-0.08860.01360.35940.07450.2122-6.33132.290821.669
124.00360.4771-0.98994.4204-0.05938.6052-0.012-0.27390.41480.14160.05170.1911-0.3497-0.1797-0.03930.11580.0358-0.00830.1719-0.01490.1658-2.505550.41612.7963
133.0692-1.08730.23043.22790.65631.5037-0.0066-0.35160.22690.1451-0.040.23880.0005-0.36390.04080.1039-0.01530.00120.231-0.01190.1545-8.206445.3112.4866
142.925-1.9246-2.99252.69141.71563.116-0.3946-0.61230.45210.60770.07990.4896-0.7282-0.727-0.04440.36880.17670.01350.4884-0.16940.3412-11.584654.413316.0465
156.3895-1.8919-2.11856.39374.1887.21910.0581-0.10350.1511-0.13320.11140.0329-0.19280.3111-0.16510.1630.0042-0.01550.16980.0190.12614.838145.84757.4052
162.88492.40761.0163.0469-0.97593.6231-0.04510.5155-0.0672-0.30590.0978-0.01440.03230.2305-0.04290.21630.0283-0.00560.21740.00290.13010.645637.6429-1.7783
176.71682.0887-0.74972.31-1.1799.36360.0405-0.1858-0.22640.02650.06330.61680.5784-0.8152-0.06740.2493-0.076-0.02520.21710.01480.2485-13.234229.42964.5709
183.50994.71682.56458.84950.60716.22270.2633-0.4891-0.44730.0911-0.1684-0.72180.23520.0651-0.08690.17510.0536-0.03980.1552-0.00620.23086.835231.883110.8828
192.07630.36750.97082.35370.23112.91450.0571-0.15430.02380.1178-0.05640.26630.3253-0.2374-0.00970.2162-0.0463-0.00750.1728-0.01190.170933.511833.197623.1768
202.05270.08470.7053.19020.28772.56050.0775-0.29110.0820.5044-0.07260.12760.1293-0.10520.02120.1893-0.0428-0.00380.1753-0.01850.130636.930237.074132.5219
211.60130.34790.50081.81370.7853.357-0.0010.08970.16860.00750.027-0.0643-0.1050.24580.03890.1827-0.0243-0.04090.20630.01610.196245.523143.913222.0555
221.69680.08770.73874.44771.03222.82920.0357-0.1144-0.13940.57070.0931-0.09470.59520.1761-0.14640.33440.0118-0.08090.19880.00070.198146.729230.604734.7353
231.8715-0.81280.51082.7698-0.82463.65530.12510.1222-0.16140.0128-0.0077-0.21350.25290.4178-0.12360.15390.029-0.03640.163-0.01560.164747.242831.014622.9408
242.8864-2.97351.45355.1016-1.31444.52440.10120.0515-0.05640.2478-0.062-0.72240.65160.9571-0.00870.32580.1315-0.08660.3719-0.01590.336855.295425.01527.1707
252.40822.5405-0.07575.468-0.18352.3077-0.10560.29370.1666-0.52090.24210.2940.2674-0.0222-0.13460.17260.0081-0.0260.17460.00170.118537.135734.150715.2584
263.28612.36770.99616.806-0.135.2364-0.14290.31220.2341-0.20880.2297-0.3337-0.44090.53710.05940.2081-0.05720.00790.22710.01140.197349.579349.354416.7493
279.16186.247-4.69646.7691-3.76515.68720.0344-0.31250.14010.0632-0.13530.31460.061-0.2880.180.1812-0.0134-0.03370.224-0.02870.228331.671941.172225.052
285.3679-0.0488-0.6674.05810.05181.27530.25040.2921-0.2222-0.17510.0656-0.01710.473-0.1819-0.28580.2336-0.0932-0.03890.2020.03680.18412.085157.22417.2976
296.2676-0.48512.07113.7212-0.04762.73460.28390.3903-0.4541-0.51520.0673-0.00150.5329-0.1083-0.33690.2835-0.0804-0.01360.211-0.00010.160715.713160.9112-2.0793
303.10390.8073-0.33093.4815-0.29314.7010.1069-0.2383-0.0210.2862-0.1484-0.1782-0.19260.140.01530.1775-0.0504-0.01720.14070.01370.153921.973869.80158.4548
311.50981.7160.60542.99872.03773.12140.25290.1018-0.0213-0.56860.04480.5119-0.4098-0.5044-0.13630.2460.0169-0.08850.36780.15590.2468.488470.3756-4.1721
323.1401-0.41411.30891.8843-1.4935.7215-0.1218-0.15620.04010.08430.16980.2449-0.423-0.5603-0.14490.2104-0.0087-0.01580.2360.03770.1789.021771.00854.7629
334.8432-0.66842.0624.6453-0.78524.48-0.0314-0.34590.7750.09230.22810.6013-0.6564-1.1950.01380.26170.13120.05540.37140.05390.33985.551774.78378.0879
342.50162.4331-1.04644.6886-0.44410.59490.2253-0.3973-0.08190.3489-0.1012-0.1458-0.0007-0.2871-0.14230.208-0.0438-0.030.23680.02840.126812.769260.741515.1635
352.24711.7977-1.68965.6579-6.04387.1920.0405-0.02650.23540.7772-0.5101-0.9847-0.79060.44940.43690.332-0.1325-0.04360.27970.060.322727.284676.325213.0692
363.56490.35720.85015.97962.30155.36910.0846-0.0435-0.41750.3756-0.0846-0.57630.2110.1973-0.0230.1806-0.0472-0.01580.17930.06080.19124.030261.41189.5701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 153 )
7X-RAY DIFFRACTION7chain 'A' and (resid 154 through 164 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 20 )
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 67 )
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 85 )
13X-RAY DIFFRACTION13chain 'B' and (resid 86 through 107 )
14X-RAY DIFFRACTION14chain 'B' and (resid 109 through 121 )
15X-RAY DIFFRACTION15chain 'B' and (resid 122 through 129 )
16X-RAY DIFFRACTION16chain 'B' and (resid 130 through 138 )
17X-RAY DIFFRACTION17chain 'B' and (resid 139 through 153 )
18X-RAY DIFFRACTION18chain 'B' and (resid 154 through 164 )
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 20 )
20X-RAY DIFFRACTION20chain 'C' and (resid 21 through 40 )
21X-RAY DIFFRACTION21chain 'C' and (resid 41 through 62 )
22X-RAY DIFFRACTION22chain 'C' and (resid 63 through 74 )
23X-RAY DIFFRACTION23chain 'C' and (resid 75 through 107 )
24X-RAY DIFFRACTION24chain 'C' and (resid 109 through 121 )
25X-RAY DIFFRACTION25chain 'C' and (resid 122 through 138 )
26X-RAY DIFFRACTION26chain 'C' and (resid 139 through 153 )
27X-RAY DIFFRACTION27chain 'C' and (resid 154 through 164 )
28X-RAY DIFFRACTION28chain 'D' and (resid 2 through 20 )
29X-RAY DIFFRACTION29chain 'D' and (resid 21 through 40 )
30X-RAY DIFFRACTION30chain 'D' and (resid 41 through 62 )
31X-RAY DIFFRACTION31chain 'D' and (resid 63 through 74 )
32X-RAY DIFFRACTION32chain 'D' and (resid 75 through 97 )
33X-RAY DIFFRACTION33chain 'D' and (resid 98 through 121 )
34X-RAY DIFFRACTION34chain 'D' and (resid 122 through 138 )
35X-RAY DIFFRACTION35chain 'D' and (resid 139 through 148 )
36X-RAY DIFFRACTION36chain 'D' and (resid 149 through 163 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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