[English] 日本語
Yorodumi
- PDB-9z0y: Crystal structure of Neisseria gonorrhoeae penicillin-binding pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9z0y
TitleCrystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance mutations and three epistatic mutations
ComponentsPenicillin-binding protein 2
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / TRANSPEPTIDASE DOMAIN / N. GONORRHOEAE / ANTIBIOTIC RESISTANCE
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 FA19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsSingh, A. / Bala, S. / Davies, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI164794-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066861 United States
CitationJournal: To Be Published
Title: Interrogating the Delicate Balance between Antibiotic Resistance and Enzymatic Function in Penicillin-Binding Protein 2 Mutations from Ceftriaxone-Resistant Neisseria gonorrhoeae strain H041
Authors: Bivins, M.M. / Tomberg, J. / Bagshaw, M. / Singh, A. / Bala, S. / Davies, C. / Nicholas, R.A.
History
DepositionNov 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 2
B: Penicillin-binding protein 2


Theoretical massNumber of molelcules
Total (without water)70,7152
Polymers70,7152
Non-polymers00
Water7,224401
1
A: Penicillin-binding protein 2


Theoretical massNumber of molelcules
Total (without water)35,3571
Polymers35,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 2


Theoretical massNumber of molelcules
Total (without water)35,3571
Polymers35,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.344, 79.594, 81.369
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 35357.363 Da / Num. of mol.: 2
Mutation: A311V, I312M, V316P, T483S, F504L, N512Y, G545S, F462I, A437V, L447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA19 (bacteria) / Gene: penA, WHOF_00731, WHOF_01799C / Plasmid: PMALC2KV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0AB74EE38, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 40% PEG 600, 0.1M CHES / PH range: 9-10

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→36.25 Å / Num. obs: 99246 / % possible obs: 99.4 % / Redundancy: 7.4 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.08 / Χ2: 1.758 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.46-1.495.50.44144660.9310.9820.1890.4820.61991.1
1.49-1.516.30.41848910.9460.9860.1720.4530.64497.9
1.51-1.546.70.38249190.9610.990.1560.4140.67999.8
1.54-1.577.10.34450240.9690.9920.1370.370.699100
1.57-1.617.30.32949900.9760.9940.1290.3540.734100
1.61-1.647.50.28149260.9780.9950.110.3020.778100
1.64-1.697.50.23849940.9850.9960.0920.2560.826100
1.69-1.737.50.20750060.9880.9970.080.2220.897100
1.73-1.787.60.18449390.9870.9970.0710.1980.974100
1.78-1.847.60.15649760.9910.9980.060.1671.129100
1.84-1.917.60.13550070.9920.9980.0520.1451.313100
1.91-1.987.60.12149920.9930.9980.0470.131.585100
1.98-2.077.60.10750030.9940.9980.0410.1141.849100
2.07-2.187.60.09749760.9940.9990.0380.1042.071100
2.18-2.327.70.0949920.9950.9990.0350.0962.345100
2.32-2.57.70.08649940.9950.9990.0330.0922.722100
2.5-2.757.70.08250130.9960.9990.0320.0883.099100
2.75-3.157.70.07250110.9960.9990.0280.0773.353100
3.15-3.967.70.06250290.9970.9990.0240.0673.84100
3.96-507.50.05450980.9970.9990.0210.0583.82499.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→36.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.555 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18793 5009 5 %RANDOM
Rwork0.16172 ---
obs0.16315 94207 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å2-0.09 Å2
2--1.78 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.46→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 0 401 5273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164982
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.8276961
X-RAY DIFFRACTIONr_angle_other_deg0.671.75111480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.179542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69410862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021163
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7131.7032617
X-RAY DIFFRACTIONr_mcbond_other1.7121.7032617
X-RAY DIFFRACTIONr_mcangle_it2.3973.0613283
X-RAY DIFFRACTIONr_mcangle_other2.3973.0613284
X-RAY DIFFRACTIONr_scbond_it3.0712.1282494
X-RAY DIFFRACTIONr_scbond_other3.0712.1282495
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5723.7323666
X-RAY DIFFRACTIONr_long_range_B_refined5.81719.225704
X-RAY DIFFRACTIONr_long_range_B_other5.78618.555618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.462→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 374 -
Rwork0.223 6473 -
obs--93.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0398-0.05420.03570.29120.1550.44330.0110.01320.02120.02250.005-0.03050.0431-0.0159-0.0160.0515-0.01310.00750.02830.01360.01662.21120.2344.166
20.1836-0.0822-0.05810.24120.18850.37290.0011-0.03520.0226-0.01340.0128-0.00160.01340.0273-0.01390.02160.00380.00820.04540.00270.010914.548-0.10735.071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 574
2X-RAY DIFFRACTION2B236 - 574

+
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