[English] 日本語
Yorodumi
- PDB-6w5e: Class D beta-lactamase BSU-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w5e
TitleClass D beta-lactamase BSU-2
ComponentsBSU-2 beta-lactamase
KeywordsHYDROLASE / antibiotic resistance / beta-lactamase / Gram-positive / class D
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
MALONATE ION / Probable beta-lactamase YbxI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSmith, C.A. / Vakulenko, S.B. / Stewart, N.K. / Toth, M.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114668
CitationJournal: J.Struct.Biol. / Year: 2020
Title: A surface loop modulates activity of the Bacillus class D beta-lactamases.
Authors: Stewart, N.K. / Bhattacharya, M. / Toth, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionMar 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BSU-2 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1606
Polymers30,7301
Non-polymers4305
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.625, 47.625, 208.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein BSU-2 beta-lactamase / Probable beta-lactamase YbxI


Mass: 30729.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ybxI, ybdS, BSU02090 / Production host: Escherichia coli (E. coli) / References: UniProt: P54427, beta-lactamase
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.2 M sodium malonate pH 4.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.26→46.4 Å / Num. obs: 62108 / % possible obs: 94.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3191 / CC1/2: 0.703 / Rpim(I) all: 0.336 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CTM

5ctm


Resolution: 1.3→43.308 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1721 2824 4.96 %
Rwork0.1521 --
obs0.1532 56927 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.68 Å2 / Biso mean: 17.3284 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.3→43.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 37 211 2192
Biso mean--27.63 28.69 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052060
X-RAY DIFFRACTIONf_angle_d0.8292778
X-RAY DIFFRACTIONf_dihedral_angle_d8.0791231
X-RAY DIFFRACTIONf_chiral_restr0.08296
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.32240.2531320.18712839100
1.3224-1.34650.19991340.17362801100
1.3465-1.37240.22341630.1742788100
1.3724-1.40040.21721470.1572850100
1.4004-1.43080.17761460.1452788100
1.4308-1.46410.20181680.14872794100
1.4641-1.50070.21811530.14022835100
1.5007-1.54130.18931470.13482829100
1.5413-1.58670.20151350.13072857100
1.5867-1.63790.18611330.12892845100
1.6379-1.69640.17361730.1292808100
1.6964-1.76440.23091200.1583241284
1.7644-1.84470.19531530.14422828100
1.8447-1.94190.2565810.1798149452
1.9419-2.06360.16341070.1443228179
2.0636-2.22290.17591430.14372879100
2.2229-2.44660.17811430.15172910100
2.4466-2.80050.16771210.1625238880
2.8005-3.52820.16311630.1559287797
3.5282-43.3080.12921620.1559300094

+
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