[English] 日本語
Yorodumi
- PDB-1a7t: METALLO-BETA-LACTAMASE WITH MES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7t
TitleMETALLO-BETA-LACTAMASE WITH MES
ComponentsMETALLO-BETA-LACTAMASE
KeywordsHYDROLASE / HYDROLASE (BETA-LACTAMASE) / METALLO BETA-LACTAMASE / ZINC
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsFitzgerald, P.M.D. / Wu, J.K. / Toney, J.H.
Citation
Journal: Biochemistry / Year: 1998
Title: Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
Authors: Fitzgerald, P.M. / Wu, J.K. / Toney, J.H.
#1: Journal: Protein Expr.Purif. / Year: 1997
Title: High-Yield Expression, Purification, and Characterization of Active, Soluble Bacteroides Fragilis Metallo-Beta-Lactamase, Ccra
Authors: Toney, J.H. / Wu, J.K. / Overbye, K.M. / Thompson, C.M. / Pompliano, D.L.
History
DepositionMar 17, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METALLO-BETA-LACTAMASE
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,47310
Polymers50,7752
Non-polymers6988
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.270, 66.960, 69.480
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein METALLO-BETA-LACTAMASE / CLASS B BETA-LACTAMASE


Mass: 25387.666 Da / Num. of mol.: 2 / Mutation: A171T, D208N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: TAL3636 / Gene: CCRA / Variant: CLINICAL ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P25910, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growpH: 6.1
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 100 MM POTASSIUM ACETATE, 100 MM MES, PH 6.1
Crystal grow
*PLUS
pH: 6.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme11
210 mMsodium cacodylate11
32 mMdithiothreitol11
43 mMsodium azide11
5100 mMMES12
6100 mMpotassium acetate12
718-21 %PEG400012

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 5, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 29508 / % possible obs: 91.3 % / Observed criterion σ(I): 1 / Redundancy: 2.06 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 42.8
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 1.47 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.074 / % possible all: 73.9
Reflection shell
*PLUS
% possible obs: 73.9 % / Num. unique obs: 3950

-
Processing

Software
NameClassification
PHASESphasing
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.85→10 Å / σ(F): 1
Details: INITIAL CYCLES OF REFINEMENT WERE PERFORMED USING PROGRAM X-PLOR. 10% OF THE DATA (RANDOMLY SELECTED) WERE SET ASIDE FOR CALCULATION OF A FREE R-FACTOR. AT THE END OF THE X-PLOR PHASE OF THE ...Details: INITIAL CYCLES OF REFINEMENT WERE PERFORMED USING PROGRAM X-PLOR. 10% OF THE DATA (RANDOMLY SELECTED) WERE SET ASIDE FOR CALCULATION OF A FREE R-FACTOR. AT THE END OF THE X-PLOR PHASE OF THE REFINEMENT, THE WORKING R WAS 0.173 AND R-FREE WAS 0.242.
RfactorNum. reflection% reflection
Rwork0.151 --
obs-29267 91.3 %
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 30 337 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.961
X-RAY DIFFRACTIONp_mcangle_it1.5341.5
X-RAY DIFFRACTIONp_scbond_it1.4541
X-RAY DIFFRACTIONp_scangle_it2.3991.5
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.5
X-RAY DIFFRACTIONp_multtor_nbd0.2010.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1990.5
X-RAY DIFFRACTIONp_planar_tor2.93
X-RAY DIFFRACTIONp_staggered_tor15.520
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.93 Å / Total num. of bins used: 12 / Num. reflection obs: 2722 / Rfactor obs: 0.188

+
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