[English] 日本語
Yorodumi
- PDB-7t7d: MA-1-206-OXA-23 30s complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t7d
TitleMA-1-206-OXA-23 30s complex
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE/HYDROLASE INHIBITOR / antibiotic resistance / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / Chem-FDX / Beta-lactamase OXA-23
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSmith, C.A. / 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)1R01AI155723 United States
CitationJournal: Mbio / Year: 2022
Title: C6 Hydroxymethyl-Substituted Carbapenem MA-1-206 Inhibits the Major Acinetobacter baumannii Carbapenemase OXA-23 by Impeding Deacylation.
Authors: Stewart, N.K. / Toth, M. / Alqurafi, M.A. / Chai, W. / Nguyen, T.Q. / Quan, P. / Lee, M. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: 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)28,0652
Polymers27,6901
Non-polymers3751
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.362, 173.362, 80.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Beta-lactamase OXA-23


Mass: 27689.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: V5TGX0
#2: Chemical ChemComp-FDX / (2R,4S)-2-(1,3-dihydroxypropan-2-yl)-4-{[(3R,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-3,4-dihydro-2H-pyrrole-5-carboxylic acid


Mass: 375.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M succinic acid, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.65→39.14 Å / Num. obs: 18431 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.08 / Net I/σ(I): 20.5
Reflection shellResolution: 2.65→2.78 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2410 / CC1/2: 0.751 / Rpim(I) all: 0.542

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JF6

4jf6


Resolution: 2.65→38.76 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 889 4.88 %
Rwork0.2177 17316 -
obs0.2194 18205 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.86 Å2 / Biso mean: 88.1142 Å2 / Biso min: 51.99 Å2
Refinement stepCycle: final / Resolution: 2.65→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 24 22 1958
Biso mean--91.19 75.04 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.820.32741410.33882841298299
2.82-3.030.31541470.287228392986100
3.03-3.340.30651480.258228502998100
3.34-3.820.27511420.216828723014100
3.82-4.810.2211480.18429003048100
4.81-38.760.23781630.206630143177100
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)
10.4810.03440.21670.7439-1.54543.30530.6652-0.96910.63720.85650.5322-0.6937-0.5077-0.38940.66990.9170.1387-0.41870.923-0.8521.874214.917859.065420.3178
23.9886-0.7516-0.11561.40151.232.5739-0.0897-0.20621.11920.07810.0505-0.0422-0.1415-0.26820.00070.64840.0373-0.22360.7773-0.03010.760212.629341.86617.3468
31.8151-1.9538-0.02742.2893-0.73091.5807-0.337-0.29140.27850.73650.1984-0.75140.270.6141-0.00030.83920.1046-0.16620.83150.00340.599322.385827.661211.655
42.00540.26040.49942.68510.08282.73120.14170.39731.1534-0.2786-0.3728-0.7082-0.1360.02350.00120.71390.0395-0.06940.70740.09920.732414.929241.925-0.0144
50.47370.1585-0.12290.48120.23820.22740.2539-0.3458-0.54730.1626-0.10221.21870.5052-0.3301-0.01020.7583-0.0308-0.04470.8406-0.03670.62642.008334.78466.8392
61.2459-0.83861.32373.9036-0.07532.2088-0.3198-0.88150.92260.47320.3242-0.82610.2785-0.05540.0020.83150.1156-0.25250.8903-0.22220.906113.995141.839418.1001
71.43440.04550.20062.4388-0.52023.33690.2727-0.55821.05041.3410.4178-0.9164-0.0634-0.07540.32630.76010.0617-0.43280.7818-0.44621.286413.773547.908216.8358
80.5445-1.20670.71232.8376-1.62890.9533-0.0315-1.5666-0.4371.35960.6827-0.2188-0.0054-0.34820.23691.02720.2321-0.40661.2955-0.51631.083912.218950.920724.5229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 57 )A35 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 101 )A58 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 138 )A102 - 138
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 186 )A139 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 201 )A187 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 225 )A202 - 225
7X-RAY DIFFRACTION7chain 'A' and (resid 226 through 255 )A226 - 255
8X-RAY DIFFRACTION8chain 'A' and (resid 256 through 273 )A256 - 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