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- PDB-7e65: The crystal structure of peptidoglycan peptidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+65
TitleThe crystal structure of peptidoglycan peptidase in complex with inhibitor 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 / Chem-HXO / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4315
Polymers56,9282
Non-polymers5033
Water1,63991
1
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9023
Polymers28,4641
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13360 Å2
MethodPISA
2
B: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5292
Polymers28,4641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.441, 91.037, 100.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 20 - 274 / Label seq-ID: 1 - 255

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Peptidase M23


Mass: 28463.752 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HXO / (2S)-2-acetamido-N-[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]-3-(4-sulfamoylphenyl)propanamide


Mass: 372.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% PEG 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.65→70 Å / Num. obs: 15653 / % possible obs: 99.8 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.054 / Rrim(I) all: 0.192 / Χ2: 0.961 / Net I/σ(I): 5.1 / Num. measured all: 191812
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.710.30.9487620.920.3030.9980.88998.4
2.7-2.7410.30.8417620.9160.2680.8850.88799.5
2.74-2.811.10.8517740.9150.2620.8910.88899.6
2.8-2.8512.20.797520.940.2310.8240.91899.9
2.85-2.9212.70.7957620.9530.2280.8270.888100
2.92-2.9812.70.6717790.9660.1920.6980.914100
2.98-3.0612.90.5617720.9750.160.5840.923100
3.06-3.1412.60.487840.9730.1380.50.959100
3.14-3.2312.80.4257560.9840.1210.4420.978100
3.23-3.3412.80.3247840.9870.0930.3370.999100
3.34-3.4612.80.2657580.9930.0760.2761.05100
3.46-3.612.70.227840.9930.0640.2291.059100
3.6-3.7612.90.1957870.9950.0560.2031.04599.9
3.76-3.9612.80.1687690.9950.0490.1751.064100
3.96-4.2112.50.1337870.9970.0390.1381.08299.9
4.21-4.53120.1147860.9970.0340.1191.149100
4.53-4.9910.80.0957840.9980.030.0991.038100
4.99-5.7111.70.0968170.9980.0290.10.899100
5.71-7.1913.90.0928170.9990.0250.0950.792100
7.19-7012.60.0648770.9980.0190.0670.80999.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JMZ

6jmz


Resolution: 2.65→67.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.331 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.278 728 5 %RANDOM
Rwork0.2073 ---
obs0.2107 13879 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.98 Å2 / Biso mean: 45.936 Å2 / Biso min: 12.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å20 Å2
2--0.11 Å20 Å2
3----0.75 Å2
Refinement stepCycle: final / Resolution: 2.65→67.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 27 91 4112
Biso mean--93.87 32.24 -
Num. residues----510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194111
X-RAY DIFFRACTIONr_bond_other_d0.0040.024029
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9725539
X-RAY DIFFRACTIONr_angle_other_deg0.97639300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58424.828174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7291510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214627
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02945
Refine LS restraints NCS

Ens-ID: 1 / Number: 14816 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.718 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.294 33 -
Rwork0.209 723 -
obs--66.08 %

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