[English] 日本語
Yorodumi
- PDB-6hoo: Crystal Structure of Rationally Designed OXA-48loop18 beta-lactamase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hoo
TitleCrystal Structure of Rationally Designed OXA-48loop18 beta-lactamase
ComponentsBeta-lactamase,OXA-48loop18,Beta-lactamase
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE OXA-48loop18 / ANTIBIOTIC
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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
FLUORIDE ION / Beta-lactamase / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZavala, A. / Retailleau, P. / Dabos, L. / Naas, T. / Iorga, B.
Funding support France, 1items
OrganizationGrant numberCountry
ANR-10-LABX-33 France
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Substrate Specificity of OXA-48 after beta 5-beta 6 Loop Replacement.
Authors: Dabos, L. / Zavala, A. / Bonnin, R.A. / Beckstein, O. / Retailleau, P. / Iorga, B.I. / Naas, T.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase,OXA-48loop18,Beta-lactamase
B: Beta-lactamase,OXA-48loop18,Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41621
Polymers57,7032
Non-polymers1,71219
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-124 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.650, 126.650, 126.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-310-

F

21B-428-

HOH

-
Components

#1: Protein Beta-lactamase,OXA-48loop18,Beta-lactamase


Mass: 28851.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA-244, blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A023ZTE5, UniProt: A0A0U4UUJ9, UniProt: Q6XEC0*PLUS, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate; 0.2 M ammonium fluoride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.38→44.78 Å / Num. obs: 27195 / % possible obs: 99.7 % / Redundancy: 16.2 % / Biso Wilson estimate: 57.457 Å2 / Rrim(I) all: 0.146 / Net I/av σ(I): 0.999 / Net I/σ(I): 16.69
Reflection shellResolution: 2.38→2.53 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 4273 / CC1/2: 0.582 / Rrim(I) all: 1.84 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
BUSTER-TNT2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSVERSION Jan 26, 2018data reduction
Aimless0.6.2data scaling
MrBUMP00.9.00phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2K

4s2k


Resolution: 2.38→19.78 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1357 5 %RANDOM
Rwork0.171 ---
obs0.173 27144 99.3 %-
Displacement parametersBiso max: 181.78 Å2 / Biso mean: 61.14 Å2 / Biso min: 31.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.38→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 100 103 4268
Biso mean--71.42 56.41 -
Num. residues----502
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1494SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it4267HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion526SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5209SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4267HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5759HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion18.09
LS refinement shellResolution: 2.38→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2245 131 4.98 %
Rwork0.216 2498 -
all0.2164 2629 -
obs--93 %
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)
11.3574-0.86340.03292.5030.03521.0709-0.02320.0370.16280.1510.0194-0.1873-0.13490.1690.0037-0.026-0.0394-0.0308-0.16020.027-0.025111.5685-11.3835-27.4083
21.0747-0.1296-0.08791.7015-0.17531.6693-0.02150.268-0.1115-0.2394-0.1510.1910.0642-0.24140.1725-0.03690.0176-0.0389-0.0865-0.1008-0.0282-6.8627-33.9783-44.3014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|3 - B|251 }B3 - 251
2X-RAY DIFFRACTION2{ A|3 - A|251 }A3 - 251

+
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