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- PDB-7v6t: Crystal structure of bacterial peptidase -

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Basic information

Entry
Database: PDB / ID: 7v6t
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
CITRIC ACID / Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.495 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: 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)30,9027
Polymers30,0722
Non-polymers8315
Water2,090116
1
A: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4824
Polymers15,0361
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint1 kcal/mol
Surface area7180 Å2
MethodPISA
2
B: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4203
Polymers15,0361
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.224, 63.720, 104.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5.1 / Details: 0.2M ammonium citrate 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: 1.49→33.387 Å / Num. obs: 79540 / % possible obs: 97.5 % / Redundancy: 7.206 % / Biso Wilson estimate: 15.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.088 / Χ2: 0.944 / Net I/σ(I): 16.06
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
1.49-1.597.1180.722.9544970686763180.8780.77692
1.59-1.697.3850.5224.6546719646763260.930.56197.8
1.69-1.837.3810.3117.4843578602859040.9710.33597.9
1.83-27.350.1712.4540280556854800.990.18398.4
2-2.247.30.09918.9436566506150090.9960.10799
2.24-2.597.2290.06825.3232407452044830.9980.07399.2
2.59-3.167.1340.05230.7727279384338240.9980.05699.5
3.16-4.466.930.0439.6220860303830100.9980.04399.1
4.46-33.3876.1540.04240.1510825180817590.9980.04697.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2k1g


Resolution: 1.495→33.387 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 3771 4.74 %
Rwork0.1922 75769 -
obs0.1932 79540 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.59 Å2 / Biso mean: 18.8427 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: final / Resolution: 1.495→33.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 56 116 2183
Biso mean--29.33 24.89 -
Num. residues----250
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.495-1.51360.28191060.3198210373
1.5136-1.53350.32811350.2735277997
1.5335-1.55450.24611410.2619281097
1.5545-1.57670.26631430.2419278397
1.5767-1.60020.27241400.2289280097
1.6002-1.62520.27941420.2255284297
1.6252-1.65190.29451360.216279498
1.6519-1.68030.24641390.214277597
1.6803-1.71090.24521450.2084288598
1.7109-1.74380.23731420.2132279498
1.7438-1.77940.25731410.202284598
1.7794-1.81810.22151310.2039277298
1.8181-1.86040.24551490.196289699
1.8604-1.90690.24681380.1977278999
1.9069-1.95840.21331400.1886285198
1.9584-2.01610.23831410.1789284099
2.0161-2.08110.17911380.1734284099
2.0811-2.15550.17831380.1797284699
2.1555-2.24180.25561400.1843284099
2.2418-2.34380.22041420.1937289399
2.3438-2.46730.19171430.182286399
2.4673-2.62190.24951420.19682857100
2.6219-2.82420.22341410.19722851100
2.8242-3.10820.19291420.19742866100
3.1082-3.55750.19361480.18042901100
3.5575-4.48040.16311390.1637283499
4.4804-33.3870.19061490.1868282098

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