[English] 日本語
Yorodumi
- PDB-1btl: CRYSTAL STRUCTURE OF ESCHERICHIA COLI TEM1 BETA-LACTAMASE AT 1.8 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1btl
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI TEM1 BETA-LACTAMASE AT 1.8 ANGSTROMS RESOLUTION
ComponentsBETA-LACTAMASE TEM1
KeywordsHYDROLASE
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsJelsch, C. / Mourey, L. / Masson, J.M. / Samama, J.P.
Citation
Journal: Proteins / Year: 1993
Title: Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution.
Authors: Jelsch, C. / Mourey, L. / Masson, J.M. / Samama, J.P.
#1: Journal: Proteins / Year: 1993
Title: Crystal Structure of Escherichia Coli Tem1 Beta-Lactamase at 1.8 Resolution
Authors: Jelsch, C. / Mourey, L. / Masson, J.M. / Samama, J.P.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Crystallographic Data on E. Coli Tem1 Beta-Lactamase
Authors: Jelsch, C. / Lenfant, F. / Masson, J.M. / Samama, J.P.
#3: Journal: FEBS Lett. / Year: 1992
Title: Beta-Lactamase Tem1 of E. Coli: Crystal Structure Determination at 2.5 Angstroms Resolution
Authors: Jelsch, C. / Lenfant, F. / Masson, J.M. / Samama, J.P.
History
DepositionNov 1, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Remark 700SHEET RESIDUES GLU 48, LEU 57, AND SER 59 FORM A BETA BULGE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-LACTAMASE TEM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0802
Polymers28,9841
Non-polymers961
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.100, 64.400, 91.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 167
2: RESIDUE ASP 214 IS ASSUMED TO BE IN THE NEUTRAL FORM, SINCE IT IS HYDROGEN BONDED TO RESIDUE ASP 233.
3: ATOM OG OF RESIDUES SER 82 AND SER 285 HAVE ALTERNATE CONFORMATIONS.
4: RESIDUES GLU 48, LEU 57, AND SER 59 FORM A BETA BULGE.
5: RESIDUE MET 69 IS LOCATED NEAR THE CATALYTIC SERINE, AND IS FOUND IN A STRAINED CONFORMATION IN ALL THE STRUCTURES OF CLASS A BETA-LACTAMASES.
6: RESIDUE LEU 220 IS PART OF ONE OF THE TWO HINGE REGIONS THAT CONNECT THE TWO PROTEIN DOMAINS. THE HINGE CONFORMATION IS STRONGLY CONSTRAINED BY THE SALT BRIDGE BETWEEN ARG 222 AND ASP 233, WHICH ...6: RESIDUE LEU 220 IS PART OF ONE OF THE TWO HINGE REGIONS THAT CONNECT THE TWO PROTEIN DOMAINS. THE HINGE CONFORMATION IS STRONGLY CONSTRAINED BY THE SALT BRIDGE BETWEEN ARG 222 AND ASP 233, WHICH CAN EXPLAIN THE HICH CONFORMATIONAL ENERGY OF THE RESIDUE LEU 220 (SEE THE REPRINT OF THE ARTICLE IN PROTEINS, P372, IN HINGE REGIONS AND DOMAINS INTERFACE).

-
Components

#1: Protein BETA-LACTAMASE TEM1


Mass: 28984.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE ASP 214 IS ASSUMED TO BE IN THE NEUTRAL FORM, SINCE IT IS HYDROGEN BONDED TO RESIDUE ASP ...RESIDUE ASP 214 IS ASSUMED TO BE IN THE NEUTRAL FORM, SINCE IT IS HYDROGEN BONDED TO RESIDUE ASP 233. RESIDUE LEU 220 IS PART OF ONE OF THE TWO HINGE REGIONS THAT CONNECT THE TWO PROTEIN DOMAINS. THE HINGE CONFORMATION IS STRONGLY CONSTRAINED BY THE SALT BRIDGE BETWEEN ARG 222 AND ASP 233, WHICH CAN EXPLAIN THE HICH CONFORMATIONAL ENERGY OF THE RESIDUE LEU 220 (SEE THE REPRINT OF THE ARTICLE IN PROTEINS, P372, IN HINGE REGIONS AND DOMAINS INTERFACE). RESIDUE MET 69 IS LOCATED NEAR THE CATALYTIC SERINE, AND IS FOUND IN A STRAINED CONFORMATION IN ALL THE STRUCTURES OF CLASS A BETA-LACTAMASES. THE STRUCTURE DISPLAYS A TOPOLOGY SIMILAR TO THAT OF THE PC1 BETA-LACTAMASE OF S. AUREUS (HERZBERG, 1991, J. MOL. BIOL., 217:701-719, PROTEIN DATA BANK ENTRY 1BLM) AND TO THAT OF B. LICHENIFORMIS 749/C (KNOX ET AL., 1991, J. MOL. BIOL., 220:435-355, PROTEIN DATA BANK ENTRY 4BLM).
Sequence detailsTHE NUMBERING SCHEME CORRESPONDS TO THAT OF AMBLER, WHERE THE ACTIVE SERINE IS AT POSITION 70 ...THE NUMBERING SCHEME CORRESPONDS TO THAT OF AMBLER, WHERE THE ACTIVE SERINE IS AT POSITION 70 (AMBLER, 1980, PHIL. TRANS. R. SOC. LOND., B289:321-331).
Source detailsTHE PROTEIN USED FOR THE STRUCTURE RESOLUTION IS THE PRODUCT OF THE AMPICILLIN-RESISTANCE GENE ...THE PROTEIN USED FOR THE STRUCTURE RESOLUTION IS THE PRODUCT OF THE AMPICILLIN-RESISTANCE GENE CARRIED ON PLASMID PBR322 IN ESCHERICHIA COLI. IT DIFFERS FROM TEM1 BETA-LACTAMASE BY THE TWO MUTATIONS V84I AND A184V.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 %satammonium sulfate1drop
360 mMphosphate1drop
460 mMphosphate1reservoir
546 %ammonium sulfate1reservoir
64 %(v/v)acetone1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 22510 / % possible obs: 94.5 % / Observed criterion σ(F): 1

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→5 Å / σ(F): 1
Details: THE STRUCTURE WAS SOLVED BY MULTIPLE ISOMORPHOUS REPLACEMENT, USING FOUR HEAVY ATOM DERIVATIVES, COMBINED WITH MOLECULAR REPLACEMENT, USING THE C ALPHA COORDINATES OF THE S. AUREUS PC1 BETA- ...Details: THE STRUCTURE WAS SOLVED BY MULTIPLE ISOMORPHOUS REPLACEMENT, USING FOUR HEAVY ATOM DERIVATIVES, COMBINED WITH MOLECULAR REPLACEMENT, USING THE C ALPHA COORDINATES OF THE S. AUREUS PC1 BETA-LACTAMASE, REFINED AT 2.5 RESOLUTION (HERZBERG AND MOULT, 1987, SCIENCE, 236:694-701).
RfactorNum. reflection
Rwork0.164 -
obs0.164 22510
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 5 199 2236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d2.66
X-RAY DIFFRACTIONp_dihedral_angle_d23.1
X-RAY DIFFRACTIONp_dihedral_angle_deg1.12
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

+
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://pdbjlvh1.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