[English] 日本語
Yorodumi
- PDB-9mcz: Crystal structure of the transpeptidase domain of PBP2 from the N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mcz
TitleCrystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6884
ComponentsPenicillin-binding protein 2
KeywordsLIGASE / Neisseria gonorrhoeae cephalosporin resistance Penicillin-binding protein 2 Boronate inhibitor
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae 35/02 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 Å
AuthorsStratton, C.M. / Bala, S. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141239 United States
CitationJournal: Biorxiv / Year: 2024
Title: A new class of penicillin-binding protein inhibitors to address drug-resistant Neisseria gonorrhoeae.
Authors: Uehara, T. / Zulli, A.L. / Miller, B. / Avery, L.M. / Boyd, S.A. / Chatwin, C.L. / Chu, G.H. / Drager, A.S. / Edwards, M. / Emeigh Hart, S.G. / Myers, C.L. / Rongala, G. / Stevenson, A. / ...Authors: Uehara, T. / Zulli, A.L. / Miller, B. / Avery, L.M. / Boyd, S.A. / Chatwin, C.L. / Chu, G.H. / Drager, A.S. / Edwards, M. / Emeigh Hart, S.G. / Myers, C.L. / Rongala, G. / Stevenson, A. / Uehara, K. / Yi, F. / Wang, B. / Liu, Z. / Wang, M. / Zhao, Z. / Zhou, X. / Zhao, H. / Stratton, C.M. / Bala, S. / Davies, C. / Tkavc, R. / Jerse, A.E. / Pevear, D.C. / Burns, C.J. / Daigle, D.M. / Condon, S.M.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9202
Polymers35,3311
Non-polymers5881
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.586, 60.735, 110.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Penicillin-binding protein 2 / Probable peptidoglycan D / D-transpeptidase PenA / PBP-2


Mass: 35331.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae 35/02 (bacteria) / Gene: penA / Plasmid: PMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8RR30, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-A1BJC / (3R)-3-{[(2R)-2-[(4-ethyl-2,3-dioxopiperazine-1-carbonyl)amino]-2-(4-phosphonophenyl)acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid


Mass: 588.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26BN4O11P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1 M CHES, PH 9.3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→38.9 Å / Num. obs: 27662 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.117 / Net I/σ(I): 15.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2643 / CC1/2: 0.839 / CC star: 0.955 / Rpim(I) all: 0.276 / Rrim(I) all: 0.761 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.89→38.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.896 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1337 4.833 %RANDOM
Rwork0.173 26325 --
all0.175 ---
obs-27662 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.053 Å20 Å2-0 Å2
2---0.038 Å20 Å2
3----0.015 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 41 122 2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122567
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162412
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6773491
X-RAY DIFFRACTIONr_angle_other_deg0.5311.5745610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.544515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79410429
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6111095
X-RAY DIFFRACTIONr_chiral_restr0.0790.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_nbd_refined0.2250.2449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22186
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21303
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.25
X-RAY DIFFRACTIONr_nbd_other0.1790.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.210
X-RAY DIFFRACTIONr_mcbond_it2.2812.3061306
X-RAY DIFFRACTIONr_mcbond_other2.2782.3061306
X-RAY DIFFRACTIONr_mcangle_it3.4333.4441634
X-RAY DIFFRACTIONr_mcangle_other3.4343.4471635
X-RAY DIFFRACTIONr_scbond_it3.2682.81261
X-RAY DIFFRACTIONr_scbond_other3.2692.7991255
X-RAY DIFFRACTIONr_scangle_it5.0664.0171854
X-RAY DIFFRACTIONr_scangle_other5.0654.0171855
X-RAY DIFFRACTIONr_lrange_it6.38730.0072823
X-RAY DIFFRACTIONr_lrange_other6.37629.6422803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.9410.263880.2131826X-RAY DIFFRACTION94.612
1.941-1.9940.219980.1991879X-RAY DIFFRACTION100
1.994-2.0520.247910.1881820X-RAY DIFFRACTION99.8955
2.052-2.1150.272910.1781760X-RAY DIFFRACTION99.7306
2.115-2.1840.208800.181734X-RAY DIFFRACTION99.8349
2.184-2.2610.235790.1791680X-RAY DIFFRACTION99.9432
2.261-2.3460.21900.1641593X-RAY DIFFRACTION99.7038
2.346-2.4410.178750.1631542X-RAY DIFFRACTION99.8148
2.441-2.5490.211700.1691487X-RAY DIFFRACTION98.7944
2.549-2.6730.184700.1731436X-RAY DIFFRACTION99.8012
2.673-2.8170.221610.171378X-RAY DIFFRACTION99.8612
2.817-2.9870.249690.181274X-RAY DIFFRACTION99.8513
2.987-3.1920.207620.1791231X-RAY DIFFRACTION99.7685
3.192-3.4450.206640.1831132X-RAY DIFFRACTION100
3.445-3.7710.225540.1831065X-RAY DIFFRACTION99.8216
3.771-4.2110.188560.161960X-RAY DIFFRACTION100
4.211-4.8530.158520.149830X-RAY DIFFRACTION98.2183
4.853-5.9210.204410.169726X-RAY DIFFRACTION99.0956
5.921-8.2780.207310.154595X-RAY DIFFRACTION100
8.278-38.870.081150.16377X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more