[English] 日本語
Yorodumi
- PDB-5oe0: CRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-181 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oe0
TitleCRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-181
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / antibiotic resistance / oxacillinase / OXA-48-like / carbapenemase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05000841209 Å
AuthorsLund, B.A. / Carlsen, T.J.O. / Leiros, H.K.S. / Thomassen, A.M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis.
Authors: Lund, B.A. / Thomassen, A.M. / Carlsen, T.J.O. / Leiros, H.K.S.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9194
Polymers60,7872
Non-polymers1322
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The homolog OXA-48 form dimers in solution, supported by SEC. Our DSC results with OXA-181 and OXA-48 indicate that OXA-181 is also a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-18 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.927, 143.927, 53.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 24 - 265

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and ((resid 24 and (name N or name...AA
22chain 'B'BB

-
Components

#1: Protein Beta-lactamase


Mass: 30393.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA-181 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G5CKK8, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 476 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris pH 7.0, 0.2M Ammonium sulfate 20.5 % PEG MME 5000
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.05→35.98175 Å / Num. obs: 40027 / % possible obs: 99.55 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.6502174613 Å2 / Rrim(I) all: 0.08461 / Net I/σ(I): 13.19
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.27 / Num. measured obs: 26225 / Num. unique obs: 3911 / Rrim(I) all: 0.8693 / % possible all: 99.21

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtk

5dtk


Resolution: 2.05000841209→35.98175 Å / SU ML: 0.300132202378 / Cross valid method: FREE R-VALUE / σ(F): 1.34986800148 / Phase error: 28.5063987825
RfactorNum. reflection% reflectionSelection details
Rfree0.242015913009 1971 4.94517901498 %Random selection
Rwork0.201511357357 ---
obs0.203524764137 39857 99.5752866815 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.7569216215 Å2
Refinement stepCycle: LAST / Resolution: 2.05000841209→35.98175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 6 476 4438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002759367172514058
X-RAY DIFFRACTIONf_angle_d0.5368568315895493
X-RAY DIFFRACTIONf_chiral_restr0.0432579851114576
X-RAY DIFFRACTIONf_plane_restr0.00308736927255707
X-RAY DIFFRACTIONf_dihedral_angle_d19.31868767252383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.4251011791111320.3547010560252677X-RAY DIFFRACTION99.1178546224
2.1013-2.15810.3552610173591260.3267817598522670X-RAY DIFFRACTION99.2193044713
2.1581-2.22160.3539395466671290.3010844702962719X-RAY DIFFRACTION99.3719469644
2.2216-2.29330.3177977099951170.304710707452680X-RAY DIFFRACTION99.1843971631
2.2933-2.37520.2675664571811290.2630623430322689X-RAY DIFFRACTION99.4705259442
2.3752-2.47030.3052281832711330.2509970652282711X-RAY DIFFRACTION99.5449772489
2.4703-2.58270.2757749329071460.2367618255552679X-RAY DIFFRACTION99.5770179767
2.5827-2.71880.2645023344651730.2354886830112666X-RAY DIFFRACTION99.7190024587
2.7188-2.88910.2861374771871280.2110074496162727X-RAY DIFFRACTION99.5814440181
2.8891-3.1120.2414414208941550.2154334862552680X-RAY DIFFRACTION99.7888067582
3.112-3.4250.225158060071430.1761922817722713X-RAY DIFFRACTION99.8252359315
3.425-3.92010.2252818611621500.1544054948192725X-RAY DIFFRACTION99.9652294854
3.9201-4.93690.1710968531171830.1355000583592714X-RAY DIFFRACTION100
4.9369-35.98730.2119886756881270.173024981942836X-RAY DIFFRACTION99.7979117548
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)
11.580574998010.0250774924038-0.07206461437652.274218526830.07388347625870.9827600020790.001444225428480.06117266045970.01191776708110.0695957425268-0.06705350123220.3850925242480.0694883173563-0.06504455725890.05487731779440.222313878732-0.02858289104790.009349363476460.2291147509780.03001131583680.275177522131-51.104029094140.737402583914.4485324437
22.577905600350.633170183253-0.1236470391241.96917963759-0.08873045030381.325156281230.0773986175145-0.228209424432-0.3632837578380.202685272066-0.0469357228836-0.411384006070.09351381478440.106293669475-0.01284313327450.2084707409310.00593204079326-0.06762230179610.1968491143020.03577678928140.28924255338-18.629393943739.366893898417.5150099346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 265)
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 265)

+
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