[English] 日本語
Yorodumi
- PDB-1pzo: TEM-1 Beta-Lactamase in Complex with a Novel, Core-Disrupting, Al... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pzo
TitleTEM-1 Beta-Lactamase in Complex with a Novel, Core-Disrupting, Allosteric Inhibitor
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / beta-lactamase / novel allosteric inhibitor / core-disruption
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
Chem-CBT / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHorn, J.R. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Allosteric inhibition through core disruption.
Authors: Horn, J.R. / Shoichet, B.K.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5803
Polymers28,9121
Non-polymers6682
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.887, 61.038, 88.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein Beta-lactamase TEM / E.C.3.5.2.6 / TEM-1 / TEM-2 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 / TEM-16/CAZ-7 / TEM-24/CAZ-6 / IRT-4 / ...TEM-1 / TEM-2 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 / TEM-16/CAZ-7 / TEM-24/CAZ-6 / IRT-4 / Penicillinase / TEM beta-lactamase / ampicillin resistance protein


Mass: 28911.904 Da / Num. of mol.: 1 / Mutation: M182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II-TEM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-CBT / N,N-BIS(4-CHLOROBENZYL)-1H-1,2,3,4-TETRAAZOL-5-AMINE


Mass: 334.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13Cl2N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.8 Å3/Da / Density % sol: 31.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: potassium phosphate buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8 / Method: other / Details: Wang, X., (2002) J.Mol.Biol., 320, 85.
Components of the solutions
*PLUS
Conc.: 1.5 M / Common name: sodium phosphate / Details: pH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97014 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2003 / Details: Mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97014 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 18277 / Num. obs: 17299 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4299 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98.47 %
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.408

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.80refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.667 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.193 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24697 937 5.1 %RANDOM
Rwork0.19054 ---
obs0.1934 17299 98.47 %-
all-18277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--1.41 Å20 Å2
3----0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.173 Å0.193 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 44 180 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212107
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9922851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045260
X-RAY DIFFRACTIONr_chiral_restr0.1340.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021575
X-RAY DIFFRACTIONr_nbd_refined0.3130.2969
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.270
X-RAY DIFFRACTIONr_mcbond_it1.0441.51304
X-RAY DIFFRACTIONr_mcangle_it1.75422093
X-RAY DIFFRACTIONr_scbond_it3.4613803
X-RAY DIFFRACTIONr_scangle_it5.0894.5758
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.246 74
Rwork0.188 1239
obs-1239
Software
*PLUS
Version: 5.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.023
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.94

+
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