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- PDB-4zng: X-ray crystallography of recombinant Lactococcus lactis prolidase -

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Basic information

Entry
Database: PDB / ID: 4zng
TitleX-ray crystallography of recombinant Lactococcus lactis prolidase
ComponentsProlidase
KeywordsHYDROLASE / Metalloenzyme / Pita-bread / Dipeptidase
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / aminopeptidase 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. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 ...Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / : / Prolidase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsKgosisejo, O. / Grochulski, P. / Tanaka, T.
CitationJournal: To Be Published
Title: X-ray crystallography of recombinant Lactococcus lactis prolidase
Authors: Kgosisejo, O. / Grochulski, P. / Tanaka, T.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Prolidase
B: Prolidase
A: Prolidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,68111
Polymers120,0403
Non-polymers6418
Water5,657314
1
C: Prolidase
hetero molecules

C: Prolidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1364
Polymers80,0272
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2030 Å2
ΔGint-24 kcal/mol
Surface area30840 Å2
MethodPISA
2
B: Prolidase
A: Prolidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6129
Polymers80,0272
Non-polymers5867
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-32 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.130, 76.990, 88.920
Angle α, β, γ (deg.)90.000, 112.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Prolidase


Mass: 40013.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: pepQ / 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.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: calcium acetate, sodium cacodylate, PEG 8000, glycerol
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 11, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→49.83 Å / Num. obs: 63058 / % possible obs: 99.94 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 9.48 / Net I/σ(I): 9.48
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.74 / CC1/2: 0.997 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Cootmodel building
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wy2

1wy2


Resolution: 2.25→49.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.872 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.243
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 3153 5 %RANDOM
Rwork0.2197 ---
obs0.2227 59906 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 199.39 Å2 / Biso mean: 63.044 Å2 / Biso min: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å2-0 Å2-0.04 Å2
2---1.6 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8301 0 21 314 8636

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