[English] 日本語
Yorodumi
- PDB-7rpc: X-ray crystal structure of OXA-24/40 K84D in complex with ertapenem -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rpc
TitleX-ray crystal structure of OXA-24/40 K84D in complex with ertapenem
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / carbapenem / carbapenemase / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase activity
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-6H7 / BICARBONATE ION / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsPowers, R.A. / Mitchell, J.M. / June, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489-02 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40.
Authors: Mitchell, J.M. / June, C.M. / Baggett, V.L. / Lowe, B.C. / Ruble, J.F. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A.
History
DepositionAug 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1734
Polymers27,6611
Non-polymers5123
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.828, 102.828, 87.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Beta-lactamase / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 ...Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA-24 class D beta-lactamase / OXA24 B-lactamase / Oxa40


Mass: 27660.760 Da / Num. of mol.: 1 / Mutation: K84D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690
Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-6H7 / (1S,4R,5S,6S)-3-{[(3S,5S)-5-carbamoylpyrrolidin-3-yl]sulfanyl}-6-[(1R)-1-hydroxyethyl]-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid / ertapenem


Mass: 355.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.18 Å3/Da / Density % sol: 70.56 % / Mosaicity: 0.572 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS HCL, 2.0 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 14713 / % possible obs: 96.1 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.047 / Rrim(I) all: 0.129 / Χ2: 1.028 / Net I/σ(I): 6.2 / Num. measured all: 114663
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.678.10.64814840.9470.2430.6930.919100
2.67-2.788.10.50715020.9670.190.5420.937100
2.78-2.918.20.38714960.9830.1450.4140.949100
2.91-3.068.10.31315040.9860.1170.3340.957100
3.06-3.258.10.19815020.9930.0740.2121.023100
3.25-3.580.14815190.9940.0560.1591.128100
3.5-3.856.70.1312030.9870.0580.1441.8278.8
3.85-4.417.50.0712680.9980.0280.0760.81982.4
4.41-5.567.70.05115580.9980.020.0541.02299.9
5.56-507.20.033167710.0130.0350.93799.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 2.58→46.03 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.852 / SU B: 10.302 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 737 5 %RANDOM
Rwork0.2155 ---
obs0.2188 13932 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 114.95 Å2 / Biso mean: 53.652 Å2 / Biso min: 29.68 Å2
Baniso -1Baniso -2Baniso -3
1--4.93 Å20 Å20 Å2
2---4.93 Å20 Å2
3---9.87 Å2
Refinement stepCycle: final / Resolution: 2.58→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 33 35 1961
Biso mean--79.87 52.14 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121970
X-RAY DIFFRACTIONr_bond_other_d0.0010.021
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.6522677
X-RAY DIFFRACTIONr_angle_other_deg0.0131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39624.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03815333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.699157
X-RAY DIFFRACTIONr_chiral_restr0.1260.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021506
LS refinement shellResolution: 2.58→2.648 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 62 -
Rwork0.288 1057 -
all-1119 -
obs--99.91 %

+
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://pdbjlvh1.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