[English] 日本語
Yorodumi
- PDB-6pqi: Crystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pqi
TitleCrystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime
ComponentsClass D Carbapenemase OXA-48
KeywordsHYDROLASE / Carbapenemase / Carbapenem / substrate / Hydrolyzed product
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D beta-Lactamase.
Authors: Akhtar, A. / Pemberton, O.A. / Chen, Y.
History
DepositionJul 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class D Carbapenemase OXA-48
B: Class D Carbapenemase OXA-48
C: Class D Carbapenemase OXA-48
D: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,28717
Polymers123,3084
Non-polymers1,98013
Water4,828268
1
A: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3545
Polymers30,8271
Non-polymers5274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2603
Polymers30,8271
Non-polymers4332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3194
Polymers30,8271
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3545
Polymers30,8271
Non-polymers5274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.732, 107.005, 96.196
Angle α, β, γ (deg.)90.000, 104.170, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Class D Carbapenemase OXA-48


Mass: 30826.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A482LRD5, UniProt: Q6XEC0*PLUS, beta-lactamase
#2: Chemical
ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate pH 4.6, 30%(w/v) PEG-4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 73475 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Χ2: 1.013 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.092.70.35233640.9210.2240.4190.59691
2.09-2.122.90.30734840.9370.1960.3650.60294.3
2.12-2.1630.28635660.950.1810.3390.59997.2
2.16-2.213.10.25336620.9610.1580.2990.64998.8
2.21-2.263.30.23636900.9650.1460.2780.64499.8
2.26-2.313.50.22737000.9710.1390.2670.64199.9
2.31-2.373.60.21937160.9750.1330.2570.672100
2.37-2.433.70.19636820.9820.1170.2280.682100
2.43-2.53.80.18337280.9810.1090.2130.709100
2.5-2.583.80.15836740.9850.0940.1840.749100
2.58-2.683.80.13837180.9880.0820.160.802100
2.68-2.783.80.11936820.9890.070.1380.9100
2.78-2.913.80.137050.9920.0590.1170.916100
2.91-3.063.80.09337310.9880.0560.1091.08499.9
3.06-3.253.80.08436800.9930.050.0981.31999.9
3.25-3.513.80.0737260.9940.0420.0821.54499.8
3.51-3.863.80.05737170.9950.0340.0661.626100
3.86-4.423.80.04737070.9960.0290.0551.58399.8
4.42-5.563.80.04337540.9970.0260.051.57399.8
5.56-503.70.04537890.9970.0270.0521.67399.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.86 Å41.64 Å
Translation6.86 Å41.64 Å

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.05→41.643 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.53
RfactorNum. reflection% reflection
Rfree0.2118 1995 2.72 %
Rwork0.1823 --
obs0.1832 73284 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.94 Å2 / Biso mean: 43.9058 Å2 / Biso min: 23.23 Å2
Refinement stepCycle: final / Resolution: 2.05→41.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 122 268 8444
Biso mean--52.92 44.23 -
Num. residues----984
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.09080.30751210.2641433384
2.0908-2.14730.34781380.2509493696
2.1473-2.21050.28261360.2248507599
2.2105-2.28190.24351500.21295171100
2.2819-2.36340.2441440.21185141100
2.3634-2.4580.24221330.2055129100
2.458-2.56990.25291560.20385157100
2.5699-2.70540.25981440.19725182100
2.7054-2.87480.18961420.1925162100
2.8748-3.09670.24171450.2015169100
3.0967-3.40820.23111430.1875186100
3.4082-3.90110.20481510.16165178100
3.9011-4.91370.15681380.1475220100
4.9137-41.640.16561540.16255250100

+
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