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- PDB-6xmr: X-ray crystallographic structure model of Lactococcus lactis prol... -

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Basic information

Entry
Database: PDB / ID: 6xmr
TitleX-ray crystallographic structure model of Lactococcus lactis prolidase mutant H38S
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 / 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
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)80,1446
Polymers79,9242
Non-polymers2204
Water22,4651247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-39 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.760, 85.710, 117.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 362 / Label seq-ID: 1 - 362

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 39962.230 Da / Num. of mol.: 2 / Mutation: H38S
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.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1247 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
22.550
1
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
277.152vapor diffusion, hanging drop6.70.1 M calcium acetate, 0.1 M Bis-Tris propane, 12-15% w/v PEG4000
277.151vapor diffusion, hanging drop6.750.1 M calcium acetate, 0.1 M Bis-Tris propane, 12-15% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97935 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.68→41.57 Å / Num. obs: 93477 / % possible obs: 99.99 % / Redundancy: 7.18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.117 / Net I/σ(I): 15.9
Reflection shellResolution: 1.68→1.76 Å / Redundancy: 7.45 % / Num. unique obs: 11518 / CC1/2: 0.623 / % possible all: 99.99

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.89 Å41.57 Å
Translation4.89 Å41.57 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZNG

4zng


Resolution: 1.7→41.57 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 4298 5.01 %
Rwork0.1645 81455 -
obs0.1662 85753 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.52 Å2 / Biso mean: 24.3819 Å2 / Biso min: 9.56 Å2
Refinement stepCycle: final / Resolution: 1.7→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 4 1247 6855
Biso mean--14.57 35.62 -
Num. residues----724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2190X-RAY DIFFRACTION4.989TORSIONAL
12B2190X-RAY DIFFRACTION4.989TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.32761240.276231981
1.7193-1.73960.29131260.2538238685
1.7396-1.76080.26221320.2357240985
1.7608-1.78310.25781300.233246588
1.7831-1.80650.27571280.2234249488
1.8065-1.83130.23491310.2172251189
1.8313-1.85740.29041350.2158255890
1.8574-1.88510.25571340.2109260291
1.8851-1.91460.23251430.2061258592
1.9146-1.9460.27051410.1951267894
1.946-1.97960.21671410.1802264393
1.9796-2.01550.21811410.1764269096
2.0155-2.05430.21711420.1694273895
2.0543-2.09620.17951420.1619272397
2.0962-2.14180.22081480.1619280997
2.1418-2.19160.18721460.1624277298
2.1916-2.24640.19721440.1625276197
2.2464-2.30720.20781480.1701281298
2.3072-2.37510.22421480.1622279698
2.3751-2.45170.17951510.1636282999
2.4517-2.53930.19761460.1658278599
2.5393-2.6410.19231500.1733282398
2.641-2.76120.22341500.1671282799
2.7612-2.90670.20981500.169285199
2.9067-3.08880.19051500.16012870100
3.0888-3.32720.17621530.14952898100
3.3272-3.66180.16471520.14382886100
3.6618-4.19120.16741540.13772917100
4.1912-5.27880.16261550.12222942100
Refinement TLS params.Method: refined / Origin x: 32.4357 Å / Origin y: -1.0123 Å / Origin z: -16.1359 Å
111213212223313233
T0.1168 Å2-0.0027 Å2-0.0009 Å2-0.106 Å2-0.0063 Å2--0.1191 Å2
L0.1416 °2-0.01 °2-0.0537 °2-0.0941 °2-0.0911 °2--0.1573 °2
S0.0023 Å °0.0094 Å °0.0096 Å °0.0125 Å °-0.007 Å °0.0061 Å °-0.0114 Å °0.009 Å °0.0044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 362
2X-RAY DIFFRACTION1allB1 - 362
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allS1 - 1247

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