[English] 日本語
Yorodumi
- PDB-3g4p: OXA-24 beta-lactamase at pH 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g4p
TitleOXA-24 beta-lactamase at pH 7.5
ComponentsBeta-lactamase OXA-24
KeywordsHYDROLASE / B-LACTAMASES / ENZYME MECHANISM / CARBAPENEM / RESISTANCE
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
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
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSantillana, E. / Romero, A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase
Authors: Bou, G. / Santillana, E. / Sheri, A. / Beceiro, A. / Sampson, J.M. / Kalp, M. / Bethel, C.R. / Distler, A.M. / Drawz, S.M. / Pagadala, S.R. / van den Akker, F. / Bonomo, R.A. / Romero, A. / Buynak, J.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis
Authors: Santillana, E. / Beceiro, A. / Bou, G. / Romero, A.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase OXA-24


Theoretical massNumber of molelcules
Total (without water)27,5871
Polymers27,5871
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.310, 102.310, 84.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

-
Components

#1: Protein Beta-lactamase OXA-24 / Beta-lactamase OXA-33 / Oxa40 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Beta-lactamase


Mass: 27586.660 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: oxa-24 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8RLA6, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M SODIUM ACETATE, 28% PEG 2000 MME, 0.1M HEPES (PH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2008
RadiationMonochromator: SINGLE SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.97→31.59 Å / Num. all: 32135 / Num. obs: 32064 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 24.04 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4548 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2jc7

2jc7


Resolution: 1.97→30.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.702 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24408 1619 5.1 %RANDOM
Rwork0.19685 ---
all0.1995 32135 --
obs0.19917 30384 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 167 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221977
X-RAY DIFFRACTIONr_angle_refined_deg2.4791.9572666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.71225.56888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.878157
X-RAY DIFFRACTIONr_chiral_restr0.1770.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021464
X-RAY DIFFRACTIONr_nbd_refined0.2330.2906
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.214
X-RAY DIFFRACTIONr_mcbond_it1.9241.51257
X-RAY DIFFRACTIONr_mcangle_it2.77421945
X-RAY DIFFRACTIONr_scbond_it4.3493851
X-RAY DIFFRACTIONr_scangle_it6.6134.5721
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 126 -
Rwork0.321 2148 -
obs--99.3 %

+
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