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- PDB-7e69: The crystal structure of peptidoglycan peptidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+69
TitleThe crystal structure of peptidoglycan peptidase in complex with inhibitor 3-3
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 / N-oxidanyl-4-[(4-sulfamoylphenyl)methyl]benzamide / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsChoi, Y. / Min, K.J. / Yoon, H.J. / 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)28,8353
Polymers28,4641
Non-polymers3722
Water55831
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 area13840 Å2
Unit cell
Length a, b, c (Å)115.649, 115.649, 56.614
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-HX6 / N-oxidanyl-4-[(4-sulfamoylphenyl)methyl]benzamide


Mass: 306.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→48.882 Å / Num. obs: 13306 / % possible obs: 100 % / Redundancy: 10.704 % / Biso Wilson estimate: 40.006 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.159 / Rrim(I) all: 0.167 / Χ2: 0.803 / Net I/σ(I): 16.59 / Num. measured all: 275472
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
2.59-2.7510.9040.5915.9645414416641650.9730.62100
2.75-2.9411.1960.4378.5743687390239020.9860.458100
2.94-3.1711.1290.31211.7540430363336330.9920.327100
3.17-3.4710.8140.21516.2236346336133610.9940.226100
3.47-3.8810.3160.14920.8831082301330130.9940.157100
3.88-4.489.2650.10524.2424674266326630.9950.111100
4.48-5.4710.2370.09427.3423094225622560.9960.099100
5.47-7.6911.3540.0928.1319972175917590.9960.095100
7.69-48.88210.9480.0733.43107739879840.9980.07499.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JMZ

6jmz


Resolution: 2.61→33.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.92 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 665 5 %RANDOM
Rwork0.1696 ---
obs0.1726 12639 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.82 Å2 / Biso mean: 39.671 Å2 / Biso min: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.61→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 22 31 2067
Biso mean--85.78 34.74 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192082
X-RAY DIFFRACTIONr_bond_other_d0.0060.022040
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9782803
X-RAY DIFFRACTIONr_angle_other_deg0.88134711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.385254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93824.94489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.798155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
LS refinement shellResolution: 2.61→2.676 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.345 48 -
Rwork0.209 909 -
obs--97.26 %

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