[English] 日本語
Yorodumi
- PDB-9bzr: Structure of Class A Beta-lactamase from Bordetella bronchiseptic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bzr
TitleStructure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with clavulonate
Componentsclass A Beta-lactamase, PenP superfamily
KeywordsHYDROLASE / lactamase / serine hydrolase / PenP / CSBID / Center for Structural Biology of Infectious Diseases / clavulonate / Structural Genomics
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
MALONIC ACID / Chem-TEM / Beta-lactamase
Similarity search - Component
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMaltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Sep 24, 2025Group: 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: class A Beta-lactamase, PenP superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3155
Polymers28,9141
Non-polymers4014
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.255, 41.914, 78.053
Angle α, β, γ (deg.)90.000, 116.960, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein class A Beta-lactamase, PenP superfamily


Mass: 28914.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Gene: BB2049 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A0H3LUA9, beta-lactamase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-TEM / N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE


Mass: 157.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 1.9 M Sodium malonate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 41957 / % possible obs: 97.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 20.87 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.148 / Net I/σ(I): 17.2
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.741 / Num. unique obs: 1928 / CC1/2: 0.834 / Rpim(I) all: 0.334

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.54 Å / SU ML: 0.1509 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 23.6279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 2037 4.91 %
Rwork0.1612 39448 -
obs0.1633 41485 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.85 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 26 115 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00442172
X-RAY DIFFRACTIONf_angle_d0.75782951
X-RAY DIFFRACTIONf_chiral_restr0.0644328
X-RAY DIFFRACTIONf_plane_restr0.0087405
X-RAY DIFFRACTIONf_dihedral_angle_d13.0755810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.3188990.27312118X-RAY DIFFRACTION77.49
1.43-1.460.34271400.25482475X-RAY DIFFRACTION91.88
1.46-1.50.27841430.21692592X-RAY DIFFRACTION94.51
1.5-1.550.24541360.20822598X-RAY DIFFRACTION94.73
1.55-1.60.22051510.19152523X-RAY DIFFRACTION93.27
1.6-1.650.27171260.18162658X-RAY DIFFRACTION96.6
1.65-1.720.22161600.16932644X-RAY DIFFRACTION97.33
1.72-1.80.22571680.15642655X-RAY DIFFRACTION97.72
1.8-1.890.20191450.14522674X-RAY DIFFRACTION98.53
1.89-2.010.18441350.1492703X-RAY DIFFRACTION97.83
2.01-2.170.17311240.13352750X-RAY DIFFRACTION98.9
2.17-2.380.19271300.14352729X-RAY DIFFRACTION98.79
2.38-2.730.2341240.17382730X-RAY DIFFRACTION98.79
2.73-3.440.21751160.17552782X-RAY DIFFRACTION98.67
3.44-35.540.18391400.14842817X-RAY DIFFRACTION98.5

+
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