[English] 日本語
Yorodumi
- PDB-1h8z: Crystal structure of the class D beta-lactamase OXA-13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h8z
TitleCrystal structure of the class D beta-lactamase OXA-13
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS D / OXACILLINASE / OXA-13
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPernot, L. / Frenois, F. / Rybkine, T. / L'Hermite, G. / Petrella, S. / Delettre, J. / Jarlier, V. / Collatz, E. / Sougakoff, W.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structures of the Class D B-Lactamase Oxa-13 in the Native Form and in Complex with Meropenem
Authors: Pernot, L. / Frenois, F. / Rybkine, T. / L'Hermite, G. / Petrella, S. / Delettre, J. / Jarlier, V. / Collatz, E. / Sougakoff, W.
#1: Journal: Microbiology / Year: 1998
Title: Carbapenems as Inhibitors of Oxa-13, a Novel, Integron-Encoded B-Lactamase in Pseudomonas Aeruginosa
Authors: Mugnier, P. / Podglajen, I. / Goldstein, F.W. / Collatz, E.
History
DepositionFeb 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
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)55,3817
Polymers54,9012
Non-polymers4805
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.730, 81.710, 125.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999894, 0.012941, -0.006663), (0.013574, 0.994276, -0.105978), (0.005253, -0.106057, -0.994346)
Vector: 5.133, 6.9221, 130.765)

-
Components

#1: Protein BETA-LACTAMASE / BETA-LACTAMASE OXA-13


Mass: 27450.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAE391 / Gene: BLA OXA-13 / Plasmid: PAZ304 / Gene (production host): BLA OXA-13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101 / References: UniProt: Q51400, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST NINETEEN RESIDUES (MET1-ALA19) DESCRIBED IN THE SEQUENCE DEPOSITED IN THE DATABASE TREMBL ...THE FIRST NINETEEN RESIDUES (MET1-ALA19) DESCRIBED IN THE SEQUENCE DEPOSITED IN THE DATABASE TREMBL ARE NOT PRESENT IN THE MATURE PROTEIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 5.5
Details: 15-17% (W/V) PEG 4000, 0.1M SODIUM CACODYLATE PH 5.0-5.5, 0.2M LITHIUM SULFATE, PROTEIN 12-15 MG/ML
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-15 mg/mlprotein1drop
215-17 %(w/v)PEG40001reservoir
30.1 Msodium cacodylate1reservoir
40.2 Mlithium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 47483 / % possible obs: 97.3 % / Observed criterion σ(I): 2.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.8 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 167073 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 92.8 %

-
Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMV. 6.0data reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EWZ

1ewz


Resolution: 1.8→20 Å / SU B: 2.85 / SU ML: 0.09 / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.14
Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE THE LOOP FROM ASP A 93 - GLN A 101 AND THE LOOP FROM ASP B 93 - GLN B 101 THE SIDE-CHAIN OF RESIDUE LYS ...Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE THE LOOP FROM ASP A 93 - GLN A 101 AND THE LOOP FROM ASP B 93 - GLN B 101 THE SIDE-CHAIN OF RESIDUE LYS A 182 HAS ALTERNATE CONFORMATIONS THE SIDE-CHAIN OF THE FOLLOWING RESIDUES HAS BEEN MODELLED A 92, GLU A 103, ARG A 104, LYS B 91, TRP B 92, GLU B 103, ARG B 104.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4877 10 %RANDOM
Rwork0.197 ---
obs-42571 97.3 %-
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 25 212 3909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.02
X-RAY DIFFRACTIONp_angle_d0.0210.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it5.252.5
X-RAY DIFFRACTIONp_mcangle_it6.2383.5
X-RAY DIFFRACTIONp_scbond_it6.6312.5
X-RAY DIFFRACTIONp_scangle_it8.4143.5
X-RAY DIFFRACTIONp_plane_restr0.030.03
X-RAY DIFFRACTIONp_chiral_restr0.2030.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor15.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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