[English] 日本語
Yorodumi
- PDB-3bls: AMPC BETA-LACTAMASE FROM ESCHERICHIA COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bls
TitleAMPC BETA-LACTAMASE FROM ESCHERICHIA COLI
ComponentsAMPC BETA-LACTAMASE
KeywordsCEPHALOSPORINASE / BETA-LACTAMASE / SERINE HYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
M-AMINOPHENYLBORONIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 2.3 Å
AuthorsUsher, K.C. / Shoichet, B.K. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1998
Title: Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design.
Authors: Usher, K.C. / Blaszczak, L.C. / Weston, G.S. / Shoichet, B.K. / Remington, S.J.
History
DepositionJun 4, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,4504
Polymers79,1762
Non-polymers2742
Water1,928107
1
A: AMPC BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,5881
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMPC BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,5881
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.380, 78.970, 99.300
Angle α, β, γ (deg.)90.00, 116.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99824, 0.058222, -0.011253), (0.059293, 0.977254, -0.203615), (-0.000858, -0.203924, -0.978986)
Vector: 103.5614, 1.68154, 46.09845)

-
Components

#1: Protein AMPC BETA-LACTAMASE


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASM / Gene: AMPC / Plasmid: POG0295 / Cellular location (production host): EXTRACELLULAR / Gene (production host): AMPC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-APB / M-AMINOPHENYLBORONIC ACID


Mass: 136.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8BNO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.7
Details: PROTEIN WAS CRYSTALLIZED FROM 1.7M NA/K PHOSPHATE, PH 8.7, COCRYSTALLIZED IN THE PRESENCE OF MAPB INHIBITOR. LARGER CRYSTALS WERE GROWN BY MICRO-SEEDING TECHNIQUE.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 8.7 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Msodium potassium phosphate1reservoir
210 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 35225 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3
Reflection
*PLUS
Num. all: 36886 / Num. measured all: 114023
Reflection shell
*PLUS
% possible obs: 88.3 % / Num. possible: 7324 / Num. unique obs: 6468

-
Processing

Software
NameClassification
TNTrefinement
UCSDdata reduction
UCSDdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR SUBSTITUTION
Starting model: PDB ENTRY 2BLS

2bls


Resolution: 2.3→25 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.159 --
all0.216 35707 -
obs0.159 35707 96 %
Rfree-0 -
Solvent computationSolvent model: BABINET SCALING / Bsol: 531 Å2 / ksol: 0.99 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 20 107 5707
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01957621
X-RAY DIFFRACTIONt_angle_deg2.6978242
X-RAY DIFFRACTIONt_dihedral_angle_d18.433080
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0131382
X-RAY DIFFRACTIONt_gen_planes0.0198205
X-RAY DIFFRACTIONt_it8.0157680.5
X-RAY DIFFRACTIONt_nbd0.02310120
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.40
X-RAY DIFFRACTIONt_planar_d0.0132
X-RAY DIFFRACTIONt_plane_restr0.0195

+
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