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- PDB-7v6s: Crystal structure of bacterial peptidase -

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Basic information

Entry
Database: PDB / ID: 7v6s
TitleCrystal structure of bacterial peptidase
ComponentsMurein DD-endopeptidase MepS/Murein LD-carboxypeptidase
KeywordsHYDROLASE / NlpC/P60
Function / homology
Function and homology information


muramoyltetrapeptide carboxypeptidase / muramoyltetrapeptide carboxypeptidase activity / capsule polysaccharide biosynthetic process / peptidoglycan metabolic process / peptidoglycan turnover / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell outer membrane / cell wall organization / endopeptidase activity / proteolysis
Similarity search - Function
: / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.883 Å
AuthorsKim, Y. / Lee, W.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To be published
Title: The crystal structure fre
Authors: Lee, W.C. / Lee, J. / Kim, Y.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
B: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)30,0722
Polymers30,0722
Non-polymers00
Water63135
1
A: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)15,0361
Polymers15,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)15,0361
Polymers15,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.835, 59.835, 133.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase / Lipoprotein Spr / Murein hydrolase MepS


Mass: 15035.954 Da / Num. of mol.: 2 / Fragment: peptidase / Mutation: C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: mepS, spr, yeiV, b2175, JW2163 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AFV4, muramoyltetrapeptide carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 9.1 / Details: 0.2M sodium phosphate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.88→40.34 Å / Num. obs: 36945 / % possible obs: 99.3 % / Redundancy: 10.334 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.241 / Rrim(I) all: 0.254 / Χ2: 0.814 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.999.8541.1542.2830923324131380.7621.21696.8
1.99-2.1310.9190.7354.3733302305430500.9020.77299.9
2.13-2.310.7990.5736.2830830285928550.9330.60399.9
2.3-2.5210.6820.4698.0328178263826380.9410.494100
2.52-2.8210.4560.33310.0825137240424040.9630.352100
2.82-3.2510.2020.21312.9122016215821580.9810.225100
3.25-3.989.8730.12418.4618206184418440.9890.131100
3.98-5.69.8290.10421.6114390147514640.9910.1199.3
5.6-40.349.2850.08321.1482739228910.9930.08896.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K1G

2k1g


Resolution: 1.883→40.34 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 3614 9.78 %
Rwork0.2115 33331 -
obs0.2151 20441 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.55 Å2 / Biso mean: 22.2546 Å2 / Biso min: 9.8 Å2
Refinement stepCycle: final / Resolution: 1.883→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 0 35 2021
Biso mean---22.64 -
Num. residues----248
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8834-1.90820.5018800.46377260
1.9082-1.93430.33311410.30151306100
1.9343-1.96190.31251360.27871281100
1.9619-1.99120.31471390.25241332100
1.9912-2.02230.28871390.25581280100
2.0223-2.05550.24551450.23751337100
2.0555-2.09090.30481440.22781281100
2.0909-2.1290.27811430.21621319100
2.129-2.16990.27621370.22351301100
2.1699-2.21420.26521400.22281296100
2.2142-2.26230.24071430.21791302100
2.2623-2.31490.28441400.21131311100
2.3149-2.37280.26751440.21411295100
2.3728-2.4370.28931430.21811286100
2.437-2.50870.26471430.23471338100
2.5087-2.58960.24691370.20891275100
2.5896-2.68220.32241470.21911295100
2.6822-2.78950.23331440.22531312100
2.7895-2.91650.25531450.21261309100
2.9165-3.07020.28281390.22711277100
3.0702-3.26250.22241540.20931321100
3.2625-3.51420.23741410.20651301100
3.5142-3.86760.23121360.17541288100
3.8676-4.42670.19251340.16081317100
4.4267-5.57480.161420.17311300100
5.5748-40.340.22391380.2138129999

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