[English] 日本語
Yorodumi
- PDB-9nt0: OXA-23-meropenem, pH 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nt0
TitleOXA-23-meropenem, pH 7.5
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE / OXA / antibiotic resistance / inhibitor / meropenem
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / plasma membrane
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-MER / Beta-lactamase OXA-23
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSmith, C.A. / Toth, M. / Stewart, N.K. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01 AI155723 United States
CitationJournal: To Be Published
Title: Dual Mechanism of the OXA-23 Carbapenemase Inhibition via Catalytic Lysine Decarboxylation and Water Access Restriction by the Carbapenem NA-1-157
Authors: Toth, M. / Stewart, N.K. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase OXA-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5363
Polymers31,0551
Non-polymers4822
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.991, 82.991, 85.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

-
Components

#1: Protein Beta-lactamase OXA-23


Mass: 31054.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: OXA-23, ari-1, bla-OXA-23, bla_2, bla_3, blaOXA, blaOXA-23, ABUW_0563
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4P2, beta-lactamase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-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 / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→37.87 Å / Num. obs: 39875 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 1 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Net I/σ(I): 20.7
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1950 / CC1/2: 0.625 / Rpim(I) all: 0.385

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→37.87 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1949 4.89 %
Rwork0.1672 --
obs0.1689 39822 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 31 135 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142089
X-RAY DIFFRACTIONf_angle_d1.4192840
X-RAY DIFFRACTIONf_dihedral_angle_d19.77811
X-RAY DIFFRACTIONf_chiral_restr0.091318
X-RAY DIFFRACTIONf_plane_restr0.009366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.31791190.27332652X-RAY DIFFRACTION99
1.64-1.680.2388930.23072695X-RAY DIFFRACTION100
1.68-1.730.25851410.20522678X-RAY DIFFRACTION100
1.73-1.790.23551460.18872641X-RAY DIFFRACTION100
1.79-1.850.25551570.19252668X-RAY DIFFRACTION100
1.85-1.930.22331370.19352669X-RAY DIFFRACTION100
1.93-2.020.2061770.16922636X-RAY DIFFRACTION100
2.02-2.120.22771460.16042669X-RAY DIFFRACTION100
2.12-2.260.20011240.16062709X-RAY DIFFRACTION100
2.26-2.430.20931410.16352706X-RAY DIFFRACTION100
2.43-2.670.18371260.16822727X-RAY DIFFRACTION100
2.67-3.060.20691790.16982693X-RAY DIFFRACTION100
3.06-3.850.18511300.15712789X-RAY DIFFRACTION100
3.86-37.870.1841330.15742941X-RAY DIFFRACTION100
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)
11.2408-0.4345-1.22720.8739-0.14261.6630.1325-0.11220.20250.2010.18880.06060.12890.23890.00580.2386-0.00650.00080.2423-0.03250.2298-14.9505-21.5987-1.8017
22.3167-0.3235-0.43631.32340.25340.7026-0.01250.287-0.0016-0.0412-0.0114-0.19920.00290.05780.00210.1662-0.02250.0420.24430.04820.19896.8209-27.3648-25.2426
32.49290.1718-0.55411.62780.0512.07470.04790.44160.2042-0.1834-0.0108-0.0148-0.069-0.13230.00130.15740.00780.00760.26380.06810.1833-5.5113-23.6178-26.1285
41.6903-1.2005-0.84070.95670.39162.159-0.0643-0.19740.04110.15390.0558-0.23190.15280.2374-0.00230.18210.0269-0.02790.2290.00580.1499-5.7235-27.5135-9.0921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 208 )
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 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