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- PDB-5ex2: Crystal structure of cyclophilin AquaCyp293 from Hirschia baltica -

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Basic information

Entry
Database: PDB / ID: 5ex2
TitleCrystal structure of cyclophilin AquaCyp293 from Hirschia baltica
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / cyclophilin / PPIase / Rotamase / folding helper / periplasmic
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / protein folding / metal ion binding
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / 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 cyclophilin type
Similarity search - Component
Biological speciesHirschia baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.294 Å
AuthorsJakob, R.P. / Maier, T.
CitationJournal: Plos One / Year: 2016
Title: Structural and Functional Characterization of a Novel Family of Cyclophilins, the AquaCyps.
Authors: Jakob, R.P. / Schmidpeter, P.A. / Koch, J.R. / Schmid, F.X. / Maier, T.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,3036
Polymers61,1792
Non-polymers1244
Water20,6631147
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6383
Polymers30,5891
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6653
Polymers30,5891
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.940, 72.730, 73.930
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 30589.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirschia baltica (bacteria) / Strain: ATCC 49814 / DSM 5838 / IFAM 1418 / Gene: Hbal_1421 / Plasmid: pNIC28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6XJ17, peptidylprolyl isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.53 % / Description: plate like, 100x100x20
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 % PEG20000, 20 % PEGMME550 in 0.03 M CaCl2, 0.03M MgCl2, 0.1 M Mops/Hepes-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.294→47.874 Å / Num. all: 124371 / Num. obs: 122350 / % possible obs: 97.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 9
Reflection shellResolution: 1.294→1.33 Å / Redundancy: 6 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.1 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CPL

2cpl


Resolution: 1.294→47.874 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 2461 2.01 %Random selection
Rwork0.1694 ---
obs0.1699 122350 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.294→47.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 4 1147 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084418
X-RAY DIFFRACTIONf_angle_d1.2196000
X-RAY DIFFRACTIONf_dihedral_angle_d12.2181680
X-RAY DIFFRACTIONf_chiral_restr0.048647
X-RAY DIFFRACTIONf_plane_restr0.006801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2942-1.3190.3525970.33875692X-RAY DIFFRACTION83
1.319-1.3460.28491280.28196755X-RAY DIFFRACTION99
1.346-1.37520.30411480.27466675X-RAY DIFFRACTION98
1.3752-1.40720.24971460.24946698X-RAY DIFFRACTION98
1.4072-1.44240.25461290.22936702X-RAY DIFFRACTION98
1.4424-1.48140.23341390.21016789X-RAY DIFFRACTION99
1.4814-1.5250.20561430.19096698X-RAY DIFFRACTION98
1.525-1.57430.23471270.18366749X-RAY DIFFRACTION99
1.5743-1.63050.16621410.16496759X-RAY DIFFRACTION99
1.6305-1.69580.19811440.1646703X-RAY DIFFRACTION98
1.6958-1.7730.19411390.16146807X-RAY DIFFRACTION99
1.773-1.86650.2021450.15926751X-RAY DIFFRACTION99
1.8665-1.98340.17931410.15996632X-RAY DIFFRACTION97
1.9834-2.13660.19261410.15156606X-RAY DIFFRACTION96
2.1366-2.35160.20581330.15366741X-RAY DIFFRACTION98
2.3516-2.69180.17191630.1546717X-RAY DIFFRACTION98
2.6918-3.39130.15871260.15266630X-RAY DIFFRACTION96
3.3913-47.90720.17831310.14856785X-RAY DIFFRACTION97
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)
11.6714-1.42350.50931.7709-0.36870.6574-0.00760.07430.1624-0.0237-0.0264-0.1605-0.07290.03260.0680.0957-0.01150.00080.1056-0.00540.13288.719117.872942.943
20.8625-0.23480.33880.77630.13611.0442-0.0103-0.0427-0.02460.0641-0.00110.01570.0157-0.0359-0.02050.0705-0.00580.01160.07450.00940.081111.9873-0.508648.9736
33.0055-0.8552-0.25670.58740.04080.3421-0.0614-0.08830.00850.04760.0410.05920.0203-0.05310.01010.0941-0.01680.00410.0781-0.01110.0968-5.91262.326850.2229
41.5476-0.18770.2720.4190.14860.5972-0.0107-0.0026-0.1340.030.01190.04610.02460.00520.00840.0773-0.00160.01580.0570.01240.09278.7633-2.041145.0559
52.2339-0.7540.60121.1896-0.26351.36810.03280.1822-0.159-0.0564-0.02250.0146-0.010.0836-0.0070.07720.00480.01150.06510.00180.09562.087715.177737.8512
62.47160.25430.2333.6891.29833.8163-0.16960.1952-0.3518-0.18550.02230.19940.2305-0.19420.14090.1137-0.02230.02140.12130.00610.162311.874-22.115778.2078
71.5765-0.13370.16810.5596-0.14130.6855-0.0104-0.08790.10850.0378-0.00010.0247-0.0409-0.0202-0.00140.08040.00580.02010.073-0.00240.08385.85262.625388.0184
83.82780.3131.22751.05180.58260.9177-0.01670.0252-0.1748-0.00740.0231-0.07370.06470.1053-0.00870.08780.00520.02070.08050.00870.125831.8801-6.252385.2645
91.1355-0.0356-0.08920.6503-0.15320.5595-0.01980.01780.075-0.00430.02970.0044-0.0302-0.0361-0.01670.08630.00440.0110.06910.00230.09829.60112.879982.154
101.4219-0.2359-0.42031.2327-0.00930.8526-0.02670.1416-0.094-0.08680.0066-0.05780.0298-0.05680.02520.10780.00410.00710.0885-0.02450.115216.0268-14.535775.2794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 224 )
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 266 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 95 )
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 145 )
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 224 )
10X-RAY DIFFRACTION10chain 'B' and (resid 225 through 266 )

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