[English] 日本語
Yorodumi
- PDB-9ixn: Crystal structure of OXA-10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ixn
TitleCrystal structure of OXA-10
ComponentsBeta-lactamase OXA-10
KeywordsHYDROLASE / Class D Beta-lactamase / OXA-10
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / 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/transpeptidase-like
Similarity search - Domain/homology
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLee, C.E. / Park, Y.S. / Park, H.J. / Kang, L.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017M3A9E4078017 Korea, Republic Of
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: Structural insights into alterations in the substrate spectrum of serine-beta-lactamase OXA-10 from Pseudomonas aeruginosa by single amino acid substitutions.
Authors: Lee, C.E. / Park, Y. / Park, H. / Kwak, K. / Lee, H. / Yun, J. / Lee, D. / Lee, J.H. / Lee, S.H. / Kang, L.W.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase OXA-10
B: Beta-lactamase OXA-10


Theoretical massNumber of molelcules
Total (without water)55,6732
Polymers55,6732
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-8 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.050, 103.640, 126.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27836.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Plasmid: pET-29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M Sodium formate, 0.1 M Tris-HCl pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Steady flow of liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→28.24 Å / Num. obs: 50131 / % possible obs: 99.85 % / Redundancy: 13.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.035 / Rrim(I) all: 0.13 / Net I/σ(I): 16.16
Reflection shellResolution: 1.92→1.989 Å / Num. unique obs: 4894 / Rpim(I) all: 0.386

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOF

1fof


Resolution: 1.92→28.24 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.282 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21346 2507 5 %RANDOM
Rwork0.18073 ---
obs0.18239 47625 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.101 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.92→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 0 376 4292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124012
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163821
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6335410
X-RAY DIFFRACTIONr_angle_other_deg0.5681.5668819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.257518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14810714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02917
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_it3.1733.131983
X-RAY DIFFRACTIONr_mcbond_other3.1533.1271982
X-RAY DIFFRACTIONr_mcangle_it4.4335.6132465
X-RAY DIFFRACTIONr_mcangle_other4.4335.6162466
X-RAY DIFFRACTIONr_scbond_it4.0423.4632029
X-RAY DIFFRACTIONr_scbond_other4.0423.4662030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9686.1822946
X-RAY DIFFRACTIONr_long_range_B_refined8.84933.24821
X-RAY DIFFRACTIONr_long_range_B_other8.31731.454708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 180 -
Rwork0.267 3430 -
obs--98.88 %

+
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