[English] 日本語
Yorodumi
- PDB-1axb: TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI INHIBITED WITH AN ACYL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1axb
TitleTEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI INHIBITED WITH AN ACYLATION TRANSITION STATE ANALOG
ComponentsTEM-1 BETA LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / BETA-LACTAMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
[[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER DIFFERENCE METHOD, STARTING WITH 1BTL / Resolution: 2 Å
AuthorsMaveyraud, L. / Pratt, R.F. / Samama, J.P.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of an acylation transition-state analog of the TEM-1 beta-lactamase. Mechanistic implications for class A beta-lactamases.
Authors: Maveyraud, L. / Pratt, R.F. / Samama, J.P.
History
DepositionOct 14, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TEM-1 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2292
Polymers28,9841
Non-polymers2451
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.040, 60.970, 88.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TEM-1 BETA LACTAMASE


Mass: 28984.076 Da / Num. of mol.: 1 / Mutation: VARIANT V84I, A184V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-FOS / [[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE


Mass: 245.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 32 %
Crystal growpH: 7.8
Details: BUFFER NA/K-PHOSPHATE 20MM PH 7.8 AMMONIUM SULFATE 45% SATURATION (4 DEGREES) ACETONE 4% (V/V) PROTEIN 14.5 MG/ML
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, hanging drop / Details: Jelsch, C., (1992) J. Mol. Biol., 223, 377.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
260 mMsodium phosphate1drop
310 %satammonium sulfate1drop
460 mMsodium phosphate1reservoir
546 %satammonium sulfate1reservoir
64 %aceton1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 7, 1995 / Details: DOUBLE MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.01 Å / Num. obs: 14698 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063
Reflection shellResolution: 2→2.25 Å / Redundancy: 2 % / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / % possible all: 86.24
Reflection
*PLUS
Num. measured all: 38707
Reflection shell
*PLUS
% possible obs: 86.2 % / Num. unique obs: 3909 / Num. measured obs: 5911

-
Processing

Software
NameVersionClassification
PROCESS(MSC)data collection
PROCESS(MSC)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESS(MSC)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: FOURIER DIFFERENCE METHOD, STARTING WITH 1BTL
Resolution: 2→8 Å / Rfactor Rfree error: 0.0053 / Cross valid method: THROUGHOUT / σ(F): 1
Details: A PHOSPHONYLATED SERINE RESIDUE WAS INTRODUCED IN THE ENGH & HUBER PARAMETER FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1494 10.2 %RANDOM
Rwork0.156 ---
obs0.156 14660 93.21 %-
Displacement parametersBiso mean: 28.9 Å2
Refine analyzeLuzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 15 127 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.336
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.195
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.1731.5
X-RAY DIFFRACTIONx_mcangle_it2.9982
X-RAY DIFFRACTIONx_scbond_it4.0772
X-RAY DIFFRACTIONx_scangle_it5.9092.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.228 102 9.4 %
Rwork0.224 1053 -
obs--78.58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.195

+
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