[English] 日本語
Yorodumi
- PDB-6t1h: OXA-51-like beta-lactamase OXA-66 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t1h
TitleOXA-51-like beta-lactamase OXA-66
ComponentsBeta-lactamase OXA-66
KeywordsANTIMICROBIAL PROTEIN / resistance protein / beta-lactamase / oxacillinase
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / Beta-lactamase OXA-66
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsTakebayashi, Y. / Chirgadze, D. / Henderson, S. / Warburton, P.J. / Evans, B.E.
CitationJournal: To Be Published
Title: Structure of the OXA-51-like beta-lactamase OXA-66
Authors: Takebayashi, Y. / Chirgadze, D. / Henderson, S. / Warburton, P. / Warburton, P.J. / Evans, B.E.
History
DepositionOct 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase OXA-66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7763
Polymers30,6451
Non-polymers1312
Water4,125229
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-37 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.544, 87.544, 90.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein Beta-lactamase OXA-66 / Beta-lactamase oxa66 / BlaOXA-66 / Carbapenem-hydrolyzing beta-lactamase OXA-66 / Carbapenem- ...Beta-lactamase oxa66 / BlaOXA-66 / Carbapenem-hydrolyzing beta-lactamase OXA-66 / Carbapenem-hydrolyzing oxacillinase OXA-66 / OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-66 / OXA-66 / OXA-66 carbapenemase / Oxacillinase / Penicillin-binding protein


Mass: 30645.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: bla-oxa-66, bla(OXA-66), bla-oxa66, bla_1, bla_2, blaOXA-66, blaOxa-66, oxa-66, oxa66, AB719_14180, B9X91_20195, CEJ63_17380, E2535_07655, EJB02_15170, SAMEA104305229_04225, SAMEA104305337_09008
Production host: Escherichia coli (E. coli) / References: UniProt: Q58XD2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.4 % / Description: Octahedral
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5 22.85% (v/v) PEG MME 550 0.01 M ZnSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 25, 2016 / Details: kappa
RadiationMonochromator: confocal mirror monochromator, a kappa geometry goniometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→45.06 Å / Num. obs: 21092 / % possible obs: 100 % / Redundancy: 75.4 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.165 / Net I/σ(I): 3.75
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 45.7 % / Num. unique obs: 2689 / Rpim(I) all: 0.112 / Rrim(I) all: 0.76 / % possible all: 100

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.1refinement
PDB_EXTRACT3.25data extraction
PROTEUM2data reduction
PHENIX1.1phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.772 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2236 1990 9.49 %
Rwork0.1881 --
obs0.1915 20960 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.23 Å2 / Biso mean: 27.15 Å2 / Biso min: 10.91 Å2
Refinement stepCycle: final / Resolution: 2.1→43.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 2 229 2145
Biso mean--34.92 36.19 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071961
X-RAY DIFFRACTIONf_angle_d0.8432653
X-RAY DIFFRACTIONf_chiral_restr0.053290
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d17.3611173
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.15260.29541400.247131699
2.1526-2.21080.27281360.24231334100
2.2108-2.27590.26011470.2215132099
2.2759-2.34930.2931390.23091319100
2.3493-2.43330.26511420.2201132899
2.4333-2.53070.24711310.2064132599
2.5307-2.64590.24451360.2126133899
2.6459-2.78530.24631430.191133199
2.7853-2.95980.22251430.19321356100
2.9598-3.18830.20711450.191355100
3.1883-3.5090.23621400.17971377100
3.509-4.01650.20181430.16741372100
4.0165-5.05910.17851490.1491395100
5.0591-43.7720.19811560.17981504100

+
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