[English] 日本語
Yorodumi
- PDB-6n6v: OXA-23 mutant F110A/M221A low pH form meropenem complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n6v
TitleOXA-23 mutant F110A/M221A low pH form meropenem complex
ComponentsBeta-lactamase
KeywordsHYDROLASE / carbapenemase / antibiotic resistance / mutant
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / hydrolase activity
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
meropenem, bound form / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2019
Title: Role of the Hydrophobic Bridge in the Carbapenemase Activity of Class D beta-Lactamases.
Authors: Stewart, N.K. / Smith, C.A. / Antunes, N.T. / Toth, M. / Vakulenko, S.B.
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7682
Polymers27,3831
Non-polymers3851
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.114, 44.012, 46.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Beta-lactamase / Beta-lactamase oxa23 / BlaOXA-23 / Carbapenemase OXA-23 / Class D beta-lactamase / OXA-23 / OXA-23 ...Beta-lactamase oxa23 / BlaOXA-23 / Carbapenemase OXA-23 / Class D beta-lactamase / OXA-23 / OXA-23 class D beta-lactamase / OXA23 carbapenemase / class D Beta-lactamase Oxa-23


Mass: 27382.590 Da / Num. of mol.: 1 / Fragment: UNP residues 32-273 / Mutation: F110A/M221A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, ...Gene: ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, AZE33_05250, C7G90_19950, CAS83_19595, CBE85_20255, CBI29_04474, CEJ63_03230, DV997_16620, DVA79_19285, IX87_16825, IX87_21860, LV38_03424, NG19_0098, SAMEA104305208_04008, SAMEA104305229_06308, SAMEA104305235_03908, SAMEA104305242_04084, SAMEA104305268_03570, SAMEA104305271_04290, SAMEA104305299_06196, SAMEA104305318_04148, SAMEA104305320_04271, SAMEA104305325_04185, SAMEA104305341_03854, SAMEA104305343_03919, SAMEA104305351_03822, SAMEA104305385_00775
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4P2, beta-lactamase
#2: Chemical ChemComp-KE1 / meropenem, bound form / (4R,5S)-3-{[(3R,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 0.06 M citric acid, 0.04 M bis-Tris propane, pH 4.1, 16% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→38.5 Å / Num. obs: 41640 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Net I/σ(I): 17.4
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 1964 / Rpim(I) all: 0.414 / Rrim(I) all: 1.078

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JF5

4jf5


Resolution: 1.55→36.957 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.26
RfactorNum. reflection% reflection
Rfree0.1917 2093 5.09 %
Rwork0.1722 --
obs0.1732 41131 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.39 Å2 / Biso mean: 26.2372 Å2 / Biso min: 9.14 Å2
Refinement stepCycle: final / Resolution: 1.55→36.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 26 168 2009
Biso mean--35.61 37.29 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58610.31551350.28442525266099
1.5861-1.62570.27731050.239926102715100
1.6257-1.66970.23741300.222925462676100
1.6697-1.71880.23091610.200425572718100
1.7188-1.77430.1931520.184225722724100
1.7743-1.83770.20661540.175525442698100
1.8377-1.91130.16961510.176325442695100
1.9113-1.99830.17421240.169926122736100
1.9983-2.10360.18731370.159525922729100
2.1036-2.23540.18251420.158425702712100
2.2354-2.4080.181350.169626012736100
2.408-2.65020.19061350.177826332768100
2.6502-3.03360.20471520.175526362788100
3.0336-3.82140.20461300.164626842814100
3.8214-36.96780.16751500.159728122962100
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)
11.9052-0.3795-0.7210.82350.05572.05070.10550.30380.1399-0.2041-0.0712-0.0505-0.04770.05780.00040.14330.0107-0.01180.1679-0.01360.121620.251218.5799-7.7838
20.8043-0.4451-0.7061.5611-0.16851.9574-0.0865-0.2298-0.11040.22610.0688-0.14670.35950.2302-0.00050.25170.0357-0.020.21370.0010.144212.636411.452415.2507
32.2731-0.2024-0.18981.04020.24492.59480.0125-0.0471-0.04940.11220.00290.03640.1926-0.04310.00310.1148-0.0135-0.01830.108200.086411.75916.18773.6849
41.9568-0.38030.15430.8197-0.13211.40150.04380.07460.1840.0335-0.0614-0.2172-0.05130.0918-0.00060.1069-0.00660.00140.1167-0.01980.15224.834821.4776-1.9537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 91 )A32 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 150 )A92 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 208 )A151 - 208
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 273 )A209 - 273

+
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