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- PDB-7v6u: Crystal structure of bacterial peptidase -

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Basic information

Entry
Database: PDB / ID: 7v6u
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
D-MALATE / Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 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 of bacterial DD-endopeptidase
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4646
Polymers30,0722
Non-polymers3924
Water59433
1
A: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers15,0361
Non-polymers1962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint1 kcal/mol
Surface area6260 Å2
MethodPISA
2
B: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2323
Polymers15,0361
Non-polymers1962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint0 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.871, 76.825, 58.207
Angle α, β, γ (deg.)90.000, 134.660, 90.000
Int Tables number5
Space group name H-MC121

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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 / 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: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7 / Details: 0.2M DL-Malic acid, 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: May 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.14→41.432 Å / Num. obs: 13739 / % possible obs: 95 % / Redundancy: 3.563 % / Biso Wilson estimate: 26.92 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.122 / Χ2: 0.85 / Net I/σ(I): 9.86 / Num. measured all: 48953
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
2.14-2.272.7830.4932.185045231018130.9420.60678.5
2.27-2.433.5450.3883.457498217321150.9290.45797.3
2.43-2.633.7590.2884.777472201719880.9530.33798.6
2.63-2.873.7460.1916.726964187918590.9840.22398.9
2.87-3.213.7390.1239.756289170516820.990.14498.7
3.21-3.713.7320.07715.675565151114910.9940.0998.7
3.71-4.533.6880.05321.244569126612390.9960.06397.9
4.53-6.383.6690.04722.68363610139910.9970.05597.8
6.38-41.4323.4140.04324.3819155825610.9960.05196.4

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Processing

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

2k1g


Resolution: 2.144→41.432 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 2639 10 %
Rwork0.1975 23740 -
obs0.2026 26379 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.27 Å2 / Biso mean: 30.3903 Å2 / Biso min: 11.62 Å2
Refinement stepCycle: final / Resolution: 2.144→41.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 26 33 2068
Biso mean--30.55 26.52 -
Num. residues----253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1445-2.18350.3863950.317685494964
2.1835-2.22550.42151050.30689199671
2.2255-2.27090.33161280.30151078120678
2.2709-2.32030.31791080.25541182129089
2.3203-2.37430.31241800.27231272145298
2.3743-2.43360.3021250.244113551480100
2.4336-2.49940.34481550.25561316147199
2.4994-2.57290.2461140.24461348146299
2.5729-2.6560.24481520.21991308146099
2.656-2.75090.29591850.22221218140399
2.7509-2.8610.26151040.22561403150799
2.861-2.99120.28551640.2213021466100
2.9912-3.14880.26221360.21971330146699
3.1488-3.3460.24311520.205613291481100
3.346-3.60420.23841610.20061292145399
3.6042-3.96670.24091270.16651326145399
3.9667-4.54010.19771320.13131329146199
4.5401-5.71760.18531720.133512951467100
5.7176-41.43990.17021440.1541312145699

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