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- PDB-6jn8: Structure of H216A mutant open form peptidoglycan peptidase -

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Basic information

Entry
Database: PDB / ID: 6jn8
TitleStructure of H216A mutant open form peptidoglycan peptidase
ComponentsPeptidase M23
KeywordsHYDROLASE / Peptidoglycan
Function / homologyPeptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.106 Å
AuthorsMin, K.J. / An, D.R. / Yoon, H.J. / Suh, S.W. / Lee, H.H.
Funding support Korea, Republic Of, United States, 8items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015R1A5A1008958 Korea, Republic Of
National Research Foundation (Korea)2015R1C1A1A01054842 Korea, Republic Of
National Research Foundation (Korea)2018R1A2B2008142 Korea, Republic Of
Ministry of Science, ICT and Future Planning2014M1A8A1049296 Korea, Republic Of
Ministry of Science, ICT and Future Planning2013R1A2A1A05067303 Korea, Republic Of
National Research Foundation (Korea)2018R1D1A1B07040808 Korea, Republic Of
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI090348 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61629 United States
CitationJournal: Nat Commun / Year: 2020
Title: Peptidoglycan reshaping by a noncanonical peptidase for helical cell shape in Campylobacter jejuni.
Authors: Min, K. / An, D.R. / Yoon, H.J. / Rana, N. / Park, J.S. / Kim, J. / Lee, M. / Hesek, D. / Ryu, S. / Kim, B.M. / Mobashery, S. / Suh, S.W. / Lee, H.H.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)29,5833
Polymers29,4221
Non-polymers1612
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.202, 113.202, 54.465
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: 29421.736 Da / Num. of mol.: 1 / Mutation: H216A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 200 mM potassium sodium tartrate tetrahydrate, 100 mM sodium citrate tribasic dehydrate at pH 5.6, 2.0 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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 45379 / % possible obs: 99.5 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Χ2: 2.869 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.14110.77422550.9330.2450.8121.696100
2.14-2.1810.90.74222940.9390.2370.7791.71100
2.18-2.2210.80.62722690.9550.2020.6591.862100
2.22-2.26110.58122970.9610.1840.6091.839100
2.26-2.3110.90.47422750.9730.1510.4981.931100
2.31-2.3710.80.41122900.9790.1320.4322.015100
2.37-2.4210.90.36922540.9830.1180.3872.032100
2.42-2.49110.31522770.9860.10.3312.139100
2.49-2.56110.25722950.9890.0810.2692.298100
2.56-2.65110.22922690.990.0730.2412.379100
2.65-2.74110.17522800.9930.0560.1842.644100
2.74-2.85110.1522880.9950.0480.1582.874100
2.85-2.98110.1222770.9960.0380.1263.182100
2.98-3.1410.60.09922850.9960.0320.1043.697100
3.14-3.3310.10.08222780.9970.0280.0874.136100
3.33-3.599.60.0722650.9970.0250.0754.51499.5
3.59-3.958.70.06522540.9960.0240.0694.89598.9
3.95-4.527.80.05922340.9960.0240.0644.88597.3
4.52-5.78.90.05622400.9970.0210.064.52998.4
5.7-509.80.05222030.9970.0180.0554.16796.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.106→28.3 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2134 1162 5.03 %
Rwork0.1818 --
obs0.1834 23090 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.52 Å2 / Biso mean: 51.5334 Å2 / Biso min: 25.31 Å2
Refinement stepCycle: final / Resolution: 2.106→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 6 136 2225
Biso mean--69.16 52 -
Num. residues----262
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1064-2.20220.2881310.2176274199
2.2022-2.31820.2761430.21322719100
2.3182-2.46340.29161460.2122729100
2.4634-2.65350.25721540.21442711100
2.6535-2.92030.24261450.21492749100
2.9203-3.34230.24111340.20242748100
3.3423-4.20870.18421490.1521275699
4.2087-28.30.17831600.1638277599
Refinement TLS params.Method: refined / Origin x: -27.2235 Å / Origin y: 41.3281 Å / Origin z: -0.5002 Å
111213212223313233
T0.2452 Å20.0547 Å20.0137 Å2-0.249 Å2-0.0001 Å2--0.2275 Å2
L2.5812 °20.6663 °2-0.5321 °2-1.0073 °2-0.3138 °2--2.3299 °2
S-0.1084 Å °-0.1312 Å °-0.21 Å °0.0218 Å °-0.0208 Å °-0.0528 Å °0.2573 Å °0.0544 Å °0.1077 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 300
2X-RAY DIFFRACTION1allE304
3X-RAY DIFFRACTION1allS1 - 143

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