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- PDB-7a6g: Structural characterization of L-proline amide hydrolase from Pse... -

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Basic information

Entry
Database: PDB / ID: 7a6g
TitleStructural characterization of L-proline amide hydrolase from Pseudomonas syringae
ComponentsPutative Proline iminopeptidase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD
Function / homologyProline-specific peptidase / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / peptidase activity / Alpha/Beta hydrolase fold / PHOSPHATE ION / Putative Proline iminopeptidase
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMartinez-Rodriguez, S. / Gavira, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
CitationJournal: Crystals / Year: 2022
Title: A New L-Proline Amide Hydrolase with Potential Application within the Amidase Process
Authors: Martinez-Rodriguez, S. / Contreras-Montoya, R. / Torres, J.M. / de Cienfuegos, L.A. / Gavira, J.A.
History
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Proline iminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8452
Polymers36,7501
Non-polymers951
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-9 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.428, 65.033, 85.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative Proline iminopeptidase


Mass: 36750.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ALPHA/BETA HYDROLASE FOLD, HYDROLASE
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Gene: ALO36_01328 / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0Q0CYJ4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 1.85 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: HR1#28: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000
Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→42.731 Å / Num. obs: 20614 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.083 / Rrim(I) all: 0.191 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-25.10.99614380.6360.4761.10799.9
8.94-42.734.20.0872610.9920.0440.09898.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMR

3wmr


Resolution: 1.95→42.731 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 1089 5.3 %
Rwork0.1562 19474 -
obs0.1597 20563 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.51 Å2 / Biso mean: 21.671 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 1.95→42.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 5 248 2636
Biso mean--30.16 32.35 -
Num. residues----303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9501-2.03880.261490.20612385
2.0388-2.14630.28671400.20262396
2.1463-2.28080.24621290.17492388
2.2808-2.45690.23211330.16092407
2.4569-2.70410.24211320.15942404
2.7041-3.09520.22921600.15792432
3.0952-3.89930.20121230.13392460
3.8993-42.7310.18011230.14082602
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)
10.04620.00630.06240.1114-0.07940.15590.11-0.1059-0.11290.1427-0.04230.12850.0727-0.02340.01330.12450.0267-0.00090.1257-0.01220.1476-33.3209-13.683610.901
20.5452-0.0783-0.22740.3131-0.15520.2134-0.00520.02510.0790.03740.04730.0347-0.06440.0220.00020.09370.0016-00.0823-0.00490.088-27.0908-2.13668.0628
30.0762-0.0688-0.00350.15830.00090.1430.06310.01710.0961-0.2352-0.1456-0.1137-0.12430.0051-0.00330.17750.04480.00950.11090.01480.105-25.287810.5368-16.2947
40.122-0.1709-0.12490.6503-0.27910.59420.02040.06070.0236-0.0685-0.0069-0.0482-0.03820.007300.098-0.00220.00640.0936-0.00630.1087-21.59132.3978-2.948
50.13170.11120.03330.09460.03590.05140.02880.07440.0147-0.0131-0.0322-0.07850.04580.06040.00040.08190.02340.00220.1117-0.0080.0926-16.6144-12.6317-1.1143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 34 )A3 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 141 )A35 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 189 )A142 - 189
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 275 )A190 - 275
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 305 )A276 - 305

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