[English] 日本語
Yorodumi
- PDB-5wi3: Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wi3
TitleStructure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to cefotaxime
ComponentsOXA-239
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CEFOTAXIME, C3' cleaved, open, bound form / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter sp. enrichment culture clone 8407 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsHarper, T.M. / June, C.M. / Powers, R.A. / Leonard, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI082416 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489 United States
CitationJournal: Biochem. J. / Year: 2018
Title: Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239.
Authors: Harper, T.M. / June, C.M. / Taracila, M.A. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Sep 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_host_org_strain / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 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 / 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
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: OXA-239
A: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3674
Polymers57,5722
Non-polymers7952
Water4,161231
1
B: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1842
Polymers28,7861
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: OXA-239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1842
Polymers28,7861
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.095, 143.032, 44.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 31 - 273 / Label seq-ID: 11 - 253

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

-
Components

#1: Protein OXA-239


Mass: 28786.166 Da / Num. of mol.: 2 / Mutation: K82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. enrichment culture clone 8407 (environmental samples)
Gene: OXA-239 / Variant: K82D / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6YCI1, beta-lactamase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O5S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07814 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07814 Å / Relative weight: 1
ReflectionResolution: 1.81→98.1 Å / Num. obs: 57689 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.046 / Net I/σ(I): 13.1
Reflection shellResolution: 1.811→1.817 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 542 / CC1/2: 0.873 / Rpim(I) all: 0.505 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0X

4k0x


Resolution: 1.81→80.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.389 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20458 2827 4.9 %RANDOM
Rwork0.17993 ---
obs0.18115 54798 99.75 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.969 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.81→80.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 52 231 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193925
X-RAY DIFFRACTIONr_bond_other_d0.0020.023605
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9635332
X-RAY DIFFRACTIONr_angle_other_deg1.00338350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9225.795176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44715676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.21514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6672.3311951
X-RAY DIFFRACTIONr_mcbond_other2.6592.331950
X-RAY DIFFRACTIONr_mcangle_it3.7163.4742443
X-RAY DIFFRACTIONr_mcangle_other3.723.4752444
X-RAY DIFFRACTIONr_scbond_it3.8822.7011974
X-RAY DIFFRACTIONr_scbond_other3.8812.7041975
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8523.9182885
X-RAY DIFFRACTIONr_long_range_B_refined8.19829.0294424
X-RAY DIFFRACTIONr_long_range_B_other8.19729.0364425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14926 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 212 -
Rwork0.331 4007 -
obs--100 %
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)
11.8817-0.3253-0.41986.02750.17451.7863-0.0657-0.1289-0.1656-0.2923-0.08720.13090.12010.08740.15290.0388-0.01020.01450.06820.03210.0959-24.1872.557-11.908
23.30910.1201-0.75571.54360.32221.85670.0519-0.10050.11180.130.0251-0.0663-0.09790.2215-0.07690.0266-0.0058-0.01590.0447-0.01620.043-8.28334.006-0.068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B31 - 273
2X-RAY DIFFRACTION2A31 - 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