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- PDB-7e60: The crystal structure of peptidoglycan peptidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+60
TitleThe crystal structure of peptidoglycan peptidase in complex with inhibitor 1
ComponentsPeptidase M23
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-Inhibitor complex
Function / homologyGlucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta / Chem-HX9 / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsMin, K. / Yoon, H.J. / Choi, Y. / Lee, H.H.
CitationJournal: Commun Biol / Year: 2022
Title: Structure-based inhibitor design for reshaping bacterial morphology
Authors: Choi, Y. / Park, J.S. / Kim, J. / Min, K. / Mahasenan, K. / Kim, C. / Yoon, H.J. / Lim, S. / Cheon, D.H. / Lee, Y. / Ryu, S. / Mobashery, S. / Kim, B.M. / Lee, H.H.
History
DepositionFeb 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8903
Polymers28,4641
Non-polymers4262
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13590 Å2
Unit cell
Length a, b, c (Å)115.531, 115.531, 55.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Peptidase M23


Mass: 28463.752 Da / Num. of mol.: 1 / Mutation: H247A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A8118_01115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J6PWI8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HX9 / (2~{R},6~{S})-2,6-diacetamido-7-[[(2~{R})-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-7-oxidanylidene-heptanoic acid


Mass: 360.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N4O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium 7.5, 1.4 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.784 Å / Num. obs: 18355 / % possible obs: 100 % / Redundancy: 8.764 % / Biso Wilson estimate: 45.403 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.113 / Χ2: 1.26 / Net I/σ(I): 15.67 / Num. measured all: 371451
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
2.2-2.339.0720.954262679692169090.7721.01199.8
2.33-2.499.0360.6942.9557534636763670.8620.736100
2.49-2.698.9540.4624.653696599759970.9450.49100
2.69-2.958.760.2648.1648340551855180.9810.28100
2.95-3.298.1050.13715.2740612501150110.9940.146100
3.29-3.87.9650.06927.9934710435843580.9970.075100
3.8-4.659.2050.04842.3134575375637560.9990.051100
4.65-6.549.0370.04743.1225809285628560.9990.05100
6.54-48.7848.3670.0448.6413496162116130.9990.04299.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JMZ

6jmz


Resolution: 2.24→37.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.113 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1838 10 %RANDOM
Rwork0.1892 ---
obs0.1938 16515 88.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.3 Å2 / Biso mean: 29.303 Å2 / Biso min: 10.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.24→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 26 148 2188
Biso mean--66.84 34.32 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132084
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171987
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6582803
X-RAY DIFFRACTIONr_angle_other_deg1.2791.5984635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1185254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04124.14994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.647155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
LS refinement shellResolution: 2.24→2.296 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.346 131 -
Rwork0.267 1159 -
obs--84.92 %

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