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- PDB-7k3u: X-ray crystallographic structure model of Lactococcus lactis prol... -

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Basic information

Entry
Database: PDB / ID: 7k3u
TitleX-ray crystallographic structure model of Lactococcus lactis prolidase mutant R293S
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: 2.7 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
DepositionSep 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: 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
C: Aminopeptidase P family protein
D: Aminopeptidase P family protein
E: Aminopeptidase P family protein
F: Aminopeptidase P family protein
G: Aminopeptidase P family protein
H: Aminopeptidase P family protein
I: Aminopeptidase P family protein
J: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,99135
Polymers399,43210
Non-polymers1,55925
Water6,846380
1
A: Aminopeptidase P family protein
hetero molecules

E: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1987
Polymers79,8862
Non-polymers3125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area2810 Å2
ΔGint-41 kcal/mol
Surface area29990 Å2
MethodPISA
2
B: Aminopeptidase P family protein
hetero molecules

F: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1987
Polymers79,8862
Non-polymers3125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area2490 Å2
ΔGint-39 kcal/mol
Surface area30600 Å2
MethodPISA
3
C: Aminopeptidase P family protein
D: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2908
Polymers79,8862
Non-polymers4046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-40 kcal/mol
Surface area30350 Å2
MethodPISA
4
G: Aminopeptidase P family protein
hetero molecules

J: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1987
Polymers79,8862
Non-polymers3125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_344-x-2,y-1/2,-z-11
Buried area2390 Å2
ΔGint-38 kcal/mol
Surface area30500 Å2
MethodPISA
5
H: Aminopeptidase P family protein
I: Aminopeptidase P family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1066
Polymers79,8862
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-39 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.300, 80.000, 187.150
Angle α, β, γ (deg.)90.000, 102.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aminopeptidase P family protein / Peptidase M24 family protein / Prolidase / Xaa-Pro dipeptidase


Mass: 39943.184 Da / Num. of mol.: 10 / Mutation: R293S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: pepQ, AMHIJAGA_00052, BW151_08640, FNJ58_07375 / 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.: 20 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M calcium acetate, 0.1 M Bis-Tris propane, 15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→49.19 Å / Num. obs: 116597 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 11587 / CC1/2: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZNG

4zng


Resolution: 2.7→49.19 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 5826 5 %
Rwork0.1984 110707 -
obs0.2029 116533 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.72 Å2 / Biso mean: 65.9243 Å2 / Biso min: 26.98 Å2
Refinement stepCycle: final / Resolution: 2.7→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28010 0 90 380 28480
Biso mean--72.9 45.96 -
Num. residues----3620
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7-2.73070.3771940.29923683
2.7307-2.76280.37441950.27543705
2.7628-2.79650.34171910.2673618
2.7965-2.83190.3791950.27993714
2.8319-2.86910.39231930.29453661
2.8691-2.90840.37231900.28213621
2.9084-2.950.38061950.27663689
2.95-2.9940.40021920.26293664
2.994-3.04080.34531940.25753677
3.0408-3.09060.36821940.24453684
3.0906-3.14390.36041910.24493642
3.1439-3.20110.35921970.24743737
3.2011-3.26260.35111910.24833617
3.2626-3.32920.33631960.2483729
3.3292-3.40160.36181920.23783649
3.4016-3.48070.32921940.21813698
3.4807-3.56770.29451930.20763653
3.5677-3.66420.29851940.20273681
3.6642-3.77190.31721930.19783685
3.7719-3.89360.27341940.183678
3.8936-4.03270.30131950.18773696
4.0327-4.19410.25421950.17583709
4.1941-4.38490.27661930.15883671
4.3849-4.61590.21921960.14923733
4.6159-4.90490.23081950.15153693
4.9049-5.28320.27171940.16313697
5.2832-5.81410.25071970.16393734
5.8141-6.65360.23041980.16523768
6.6536-8.37620.22071960.17193717
Refinement TLS params.Method: refined / Origin x: -91.1986 Å / Origin y: -27.9509 Å / Origin z: -47.2757 Å
111213212223313233
T0.4276 Å2-0.0047 Å20.0068 Å2-0.3744 Å20.0272 Å2--0.4097 Å2
L0.113 °20.0112 °20.0515 °2-0.0237 °20.0086 °2--0.1143 °2
S-0.0014 Å °-0.0904 Å °-0.0134 Å °0.0575 Å °0.017 Å °0.0342 Å °0.0333 Å °-0.0937 Å °-0.0161 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 362
2X-RAY DIFFRACTION1allB1 - 362
3X-RAY DIFFRACTION1allC1 - 362
4X-RAY DIFFRACTION1allD1 - 362
5X-RAY DIFFRACTION1allE1 - 362
6X-RAY DIFFRACTION1allF1 - 362
7X-RAY DIFFRACTION1allG1 - 362
8X-RAY DIFFRACTION1allH1 - 362
9X-RAY DIFFRACTION1allI1 - 362
10X-RAY DIFFRACTION1allJ1 - 362
11X-RAY DIFFRACTION1allK1 - 6
12X-RAY DIFFRACTION1allK7 - 17
13X-RAY DIFFRACTION1allK18
14X-RAY DIFFRACTION1allK19 - 20
15X-RAY DIFFRACTION1allL2 - 6
16X-RAY DIFFRACTION1allS1 - 425

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