[English] 日本語
Yorodumi
- PDB-4yfm: Class A beta-lactamase from Mycobacterium abscessus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yfm
TitleClass A beta-lactamase from Mycobacterium abscessus
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / clavulanate / carbapenem / Mycobacterium tuberculosis
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / 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
ACETATE ION / : / Beta-lactamase (Penicillinase)
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSoroka, D. / Li de la Sierra-Gallay, I. / Dubee, V. / van Tilbeurgh, H. / Arthur, M.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: Hydrolysis of Clavulanate by Mycobacterium tuberculosis beta-Lactamase BlaC Harboring a Canonical SDN Motif.
Authors: Soroka, D. / Li de la Sierra-Gallay, I. / Dubee, V. / Triboulet, S. / van Tilbeurgh, H. / Compain, F. / Ballell, L. / Barros, D. / Mainardi, J.L. / Hugonnet, J.E. / Arthur, M.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)60,5706
Polymers60,2682
Non-polymers3024
Water8,449469
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2853
Polymers30,1341
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2853
Polymers30,1341
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.490, 65.210, 107.420
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase


Mass: 30133.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: LA62_14585 / Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: A0A089SRR3, UniProt: B1MCI3*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium acetate, 0.1 MES (pH 6.5), 32% polyethylene glycol monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.4→41.5 Å / Num. obs: 93890 / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.29
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.34 / % possible all: 73.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSNovember 3, 2014data reduction
XSCALENovember 3, 2014data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.4→41.45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.224 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1712 4695 5 %RANDOM
Rwork0.14307 ---
obs0.14447 89195 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20.68 Å2
2---0.36 Å20 Å2
3---1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.4→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 20 469 4441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194030
X-RAY DIFFRACTIONr_bond_other_d0.0010.023900
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9775472
X-RAY DIFFRACTIONr_angle_other_deg0.94838960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00223.529170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29515680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0861540
X-RAY DIFFRACTIONr_chiral_restr0.1330.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
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_it1.6171.5712080
X-RAY DIFFRACTIONr_mcbond_other1.4961.5692077
X-RAY DIFFRACTIONr_mcangle_it2.1232.3522594
X-RAY DIFFRACTIONr_mcangle_other2.1232.3532595
X-RAY DIFFRACTIONr_scbond_it3.321.9161950
X-RAY DIFFRACTIONr_scbond_other3.3091.9161950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.852.742879
X-RAY DIFFRACTIONr_long_range_B_refined6.18914.4154904
X-RAY DIFFRACTIONr_long_range_B_other5.9513.7044697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 236 -
Rwork0.319 4473 -
obs--64.68 %

+
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