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- PDB-1w74: X-ray structure of peptidyl-prolyl cis-trans isomerase A, PpiA, R... -

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Basic information

Entry
Database: PDB / ID: 1w74
TitleX-ray structure of peptidyl-prolyl cis-trans isomerase A, PpiA, Rv0009, from Mycobacterium tuberculosis.
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
KeywordsISOMERASE / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / CYCLOPHILIN / PPIASE / RV0009 / ROTAMASE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


cell wall / response to iron ion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHenriksson, L.M. / Johansson, P. / Unge, T. / Mowbray, S.L.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: X-Ray Structure of Peptidyl-Prolyl Cis-Trans Isomerase a from Mycobacterium Tuberculosis
Authors: Henriksson, L.M. / Johansson, P. / Unge, T. / Mowbray, S.L.
History
DepositionAug 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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 A
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A


Theoretical massNumber of molelcules
Total (without water)40,6072
Polymers40,6072
Non-polymers00
Water23413
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A


Theoretical massNumber of molelcules
Total (without water)20,3031
Polymers20,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A


Theoretical massNumber of molelcules
Total (without water)20,3031
Polymers20,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.349, 65.349, 102.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7467, 0.6651, -0.002), (-0.6648, -0.7464, -0.0301), (-0.0215, -0.0212, 0.9995)
Vector: 18.9808, 83.1854, -10.3675)

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A / PPIASE A / ROTAMASE A


Mass: 20303.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR T7/CT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P71578, UniProt: P9WHW3*PLUS, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPPIASES ACCELERATE THE FOLDING OF PROTEINS. IT CATALYZES THE CIS-TRANS ISOMERIZATION OF PROLINE ...PPIASES ACCELERATE THE FOLDING OF PROTEINS. IT CATALYZES THE CIS-TRANS ISOMERIZATION OF PROLINE IMIDIC PEPTIDE BONDS IN OLIGOPEPTIDES
Sequence detailsTHE PROTEIN WAS EXPRESSED WITH AN ADDITIONAL 6-HISTIDINE TAG (MAHHHHHHSG, G REPLACING THE INITIAL M) ...THE PROTEIN WAS EXPRESSED WITH AN ADDITIONAL 6-HISTIDINE TAG (MAHHHHHHSG, G REPLACING THE INITIAL M), WHICH IS NOT PRESENT IN THE MODEL.

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6
Details: PROTEIN WAS CO-CRYSTALLIZED WITH THE PEPTIDE HAGPIA (FINAL CONCENTRATION 1 MM) FROM 30% PEG-200, 5% PEG-3000, 0.1 M MES-HCL PH 6.0; THEN SOAKED IN THE RESERVOIR SOLUTION PLUS 1 MM HAGPIA.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2004 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→32.62 Å / Num. obs: 14896 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AWR

1awr


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.999 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 756 5 %RANDOM
Rwork0.212 ---
obs0.213 14230 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.82 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å22.6 Å20 Å2
2--5.21 Å20 Å2
3----7.81 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 13 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212624
X-RAY DIFFRACTIONr_bond_other_d0.0040.022302
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9343564
X-RAY DIFFRACTIONr_angle_other_deg1.01135366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023018
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02540
X-RAY DIFFRACTIONr_nbd_refined0.1850.2456
X-RAY DIFFRACTIONr_nbd_other0.250.22543
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21413
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3950.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.51688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37722710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7793936
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2684.5854
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 66
Rwork0.308 996

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