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- PDB-7n02: X-ray crystallographic structure model of Lactococcus lactis prol... -

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Basic information

Entry
Database: PDB / ID: 7n02
TitleX-ray crystallographic structure model of Lactococcus lactis prolidase mutant D36S
ComponentsAminopeptidase P family protein
KeywordsHYDROLASE / proline-specific / allosteric behaviour / substrate inhibition / dipeptidase / lactic acid bacteria / debittering of fermented foods
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / metal ion binding
Similarity search - Function
: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
: / Peptidase M24 family protein
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsXu, S. / Grochulski, P. / Tanaka, T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-06209-2016 Canada
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2017
Title: Crystallographic structure of recombinant Lactococcus lactis prolidase to support proposed structure-function relationships.
Authors: Kgosisejo, O. / Chen, J.A. / Grochulski, P. / Tanaka, T.
History
DepositionMay 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase P family protein
B: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1906
Polymers79,9712
Non-polymers2204
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-37 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.120, 87.270, 119.400
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 Aminopeptidase P family protein / M24 family metallopeptidase / Peptidase M24 family protein / Prolidase / Xaa-Pro dipeptidase


Mass: 39985.289 Da / Num. of mol.: 2 / Mutation: D36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: pepQ, AMHIJAGA_00052, BW151_08640, FNJ58_07375, GTP06_13345
Production host: Escherichia coli (E. coli) / References: UniProt: A8WBX8, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium acetate, 0.1 M Bis-Tris propane, 12-15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5215 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5215 Å / Relative weight: 1
ReflectionResolution: 2.35→43.64 Å / Num. obs: 36748 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 2.35→2.47 Å / Redundancy: 6.48 % / Num. unique obs: 3603 / CC1/2: 0.517 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZNG

4zng


Resolution: 2.35→43.635 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2699 1777 5.01 %
Rwork0.2122 33726 -
obs0.2152 35503 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.21 Å2 / Biso mean: 57.6394 Å2 / Biso min: 34.79 Å2
Refinement stepCycle: final / Resolution: 2.35→43.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 4 178 5790
Biso mean--52.26 56.28 -
Num. residues----724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.41360.7671790.7253152358
2.4136-2.48460.45771380.4064259898
2.4846-2.56480.41381400.3321264299
2.5648-2.65640.48441390.35922642100
2.6564-2.76280.42821390.317263099
2.7628-2.88850.3021410.26082665100
2.8885-3.04070.32181390.23562653100
3.0407-3.23120.27511420.23942703100
3.2312-3.48060.30111400.22752668100
3.4806-3.83070.25381410.2106268899
3.8307-4.38450.26951430.17882716100
4.3845-5.52230.1771450.14492739100

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