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- PDB-6jn7: Structure of H216A mutant closed form peptidoglycan peptidase -

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Basic information

Entry
Database: PDB / ID: 6jn7
TitleStructure of H216A mutant closed form peptidoglycan peptidase
ComponentsPeptidase M23
KeywordsHYDROLASE / Peptidoglycan
Function / homologyPeptidase M23 / Peptidase family M23 / Duplicated hybrid motif / D(-)-TARTARIC ACID / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M23
B: Peptidase M23
C: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9129
Polymers88,2653
Non-polymers6466
Water11,728651
1
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6373
Polymers29,4221
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-40 kcal/mol
Surface area13110 Å2
MethodPISA
2
B: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6373
Polymers29,4221
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-40 kcal/mol
Surface area13070 Å2
MethodPISA
3
C: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6373
Polymers29,4221
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-39 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.304, 105.632, 86.161
Angle α, β, γ (deg.)90.000, 107.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidase M23


Mass: 29421.736 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 1.1M malonic acid, 150mM ammonium citrate tribasic, 72mM succinic acid, 180mM DL-malic acid, 240mM sodium acetate, 300mM sodium formate, 96mM ammonium tartrate dibasic at pH 7.0

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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: 2.033→50 Å / Num. obs: 89706 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 31.01 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.044 / Rrim(I) all: 0.113 / Χ2: 3.124 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.086.90.6944090.8610.2820.7461.86299.1
2.08-2.117.50.61344890.930.2410.661.92100
2.11-2.157.40.52544970.9520.2070.5641.999100
2.15-2.27.50.45944720.9490.180.4942.068100
2.2-2.257.40.40944520.9660.1610.442.12100
2.25-2.37.40.35544890.970.140.3822.267100
2.3-2.357.40.30544940.9750.120.3282.306100
2.35-2.427.40.26544490.9780.1050.2852.497100
2.42-2.497.30.22344970.9860.0890.242.645100
2.49-2.577.30.20444940.9850.0810.222.79100
2.57-2.667.20.17444890.990.070.1883.05100
2.66-2.777.10.1444720.9920.0570.1513.297100
2.77-2.8970.12244920.9930.050.1323.57100
2.89-3.056.80.10344920.9930.0440.1123.96699.9
3.05-3.246.60.08845070.9940.0380.0964.249100
3.24-3.496.40.07644780.9950.0330.0834.61499.9
3.49-3.846.20.07145240.9950.0310.0784.768100
3.84-4.3960.06645190.9950.030.0734.91499.9
4.39-5.5460.06145170.9960.0270.0674.71799.8
5.54-5060.05944740.9950.0270.0654.60597.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→32.696 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.1
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 4453 4.97 %RANDOM
Rwork0.1672 ---
obs0.1685 89642 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.41 Å2 / Biso mean: 36.0009 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: final / Resolution: 2.04→32.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6249 0 33 651 6933
Biso mean--48.89 44.2 -
Num. residues----786
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.04-2.05630.26631260.2174228880
2.0563-2.08050.24371640.2172819100
2.0805-2.10580.27761410.21042868100
2.1058-2.13250.21871450.19662856100
2.1325-2.16050.22951470.19242841100
2.1605-2.19010.23361440.18492832100
2.1901-2.22140.22931600.18892875100
2.2214-2.25460.22591420.18872827100
2.2546-2.28980.23161550.18032864100
2.2898-2.32730.23121490.18032886100
2.3273-2.36740.20561200.17922823100
2.3674-2.41050.22481280.18232913100
2.4105-2.45680.22611530.18412849100
2.4568-2.50690.23441440.18672872100
2.5069-2.56140.25041820.20152835100
2.5614-2.6210.23471510.19722839100
2.621-2.68650.22331530.19342869100
2.6865-2.75910.21891530.19612841100
2.7591-2.84030.24881340.20042894100
2.8403-2.93190.24591510.19942839100
2.9319-3.03660.21621470.19632876100
3.0366-3.15810.23491490.18492877100
3.1581-3.30170.20461650.16882829100
3.3017-3.47560.17261550.14992857100
3.4756-3.6930.15771400.14332890100
3.693-3.97770.15721650.14222837100
3.9777-4.37720.14941260.13332911100
4.3772-5.00860.14811400.12042891100
5.0086-6.30290.15791650.14642880100
6.3029-32.6960.16681590.1724281196
Refinement TLS params.Method: refined / Origin x: 11.579 Å / Origin y: -11.5415 Å / Origin z: 35.0087 Å
111213212223313233
T0.1666 Å20.0109 Å2-0.0083 Å2-0.187 Å20.0257 Å2--0.1881 Å2
L0.0309 °20.049 °2-0.0393 °2-0.0869 °2-0.0022 °2--0.1351 °2
S0.0262 Å °-0.0055 Å °-0.0074 Å °-0.0027 Å °-0.0065 Å °0.0211 Å °-0.0145 Å °0.043 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 281
2X-RAY DIFFRACTION1allA300
3X-RAY DIFFRACTION1allD302
4X-RAY DIFFRACTION1allB20 - 281
5X-RAY DIFFRACTION1allE300 - 302
6X-RAY DIFFRACTION1allC20 - 281
7X-RAY DIFFRACTION1allC300
8X-RAY DIFFRACTION1allF302
9X-RAY DIFFRACTION1allS1 - 673

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