[English] 日本語
Yorodumi
- PDB-9d7c: OXA-58-NA-1-157 10 min complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d7c
TitleOXA-58-NA-1-157 10 min complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / antibiotic resistance / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex
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/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CARBON DIOXIDE / Chem-Y33 / Beta-lactamase OXA-58
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsSmith, C.A. / Maggiolo, A.O. / Toth, M. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Decarboxylation of the Catalytic Lysine Residue by the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the OXA-58 Carbapenemase.
Authors: Toth, M. / Stewart, N.K. / Maggiolo, A.O. / Quan, P. / Khan, M.M.K. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,51510
Polymers125,8214
Non-polymers1,6946
Water3,747208
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4551
Non-polymers4452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8572
Polymers31,4551
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4551
Non-polymers4452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8572
Polymers31,4551
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.010, 65.771, 193.101
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Beta-lactamase


Mass: 31455.205 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-58, bla-oxa-58, bla-oxa58, GSE42_20550, P9867_20895
Production host: Escherichia coli (E. coli) / References: UniProt: Q2TR58, beta-lactamase
#2: Chemical
ChemComp-Y33 / (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid


Mass: 401.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.87 Å3/Da / Density % sol: 34.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 30% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→54.41 Å / Num. obs: 62529 / % possible obs: 91.3 % / Redundancy: 6.5 % / CC1/2: 0.981 / Rpim(I) all: 0.08 / Rrim(I) all: 0.205 / Net I/σ(I): 5.3
Reflection shellResolution: 1.94→1.98 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2799 / CC1/2: 0.558 / Rpim(I) all: 0.64

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.94→54.41 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.682 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24871 3010 4.8 %RANDOM
Rwork0.21846 ---
obs0.21995 59268 91.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.554 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20.59 Å2
2--3.31 Å20 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.94→54.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7644 0 110 208 7962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127933
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167604
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.83410727
X-RAY DIFFRACTIONr_angle_other_deg0.3661.78317458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.219535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.705101370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021861
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_it1.032.9483811
X-RAY DIFFRACTIONr_mcbond_other1.032.9483811
X-RAY DIFFRACTIONr_mcangle_it1.8065.2934748
X-RAY DIFFRACTIONr_mcangle_other1.8065.2934749
X-RAY DIFFRACTIONr_scbond_it1.043.1234122
X-RAY DIFFRACTIONr_scbond_other1.043.1244123
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8475.7025980
X-RAY DIFFRACTIONr_long_range_B_refined3.08928.618673
X-RAY DIFFRACTIONr_long_range_B_other3.06328.568656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.945→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 200 -
Rwork0.336 3727 -
obs--79.29 %

+
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