[English] 日本語
Yorodumi
- PDB-1hzo: STRUCTURE OF CLASS A CEPHALOSPORINASE FROM PROTEUS VULGARIS K1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hzo
TitleSTRUCTURE OF CLASS A CEPHALOSPORINASE FROM PROTEUS VULGARIS K1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / MIXED ALPHA/BETA / CEPHALOSPORINASE / CLASS A 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 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 speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNukaga, M. / Crichlow, G.V. / Kuzin, A.P. / Mayama, K. / Knox, J.R.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of an extended-spectrum class A beta-lactamase from Proteus vulgaris K1.
Authors: Nukaga, M. / Mayama, K. / Crichlow, G.V. / Knox, J.R.
History
DepositionJan 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE RESIDUE NUMBERING IS NOT SEQUENTIAL. Residues 57 and 59, 238 and 240, 252 and 254 are ...SEQUENCE THE RESIDUE NUMBERING IS NOT SEQUENTIAL. Residues 57 and 59, 238 and 240, 252 and 254 are covalently bound. The numbering is the accepted consensus numbering scheme for beta-lactamases. Asp24-asn25-asn26 are not seen in the density at the N-terminus, and the last four residues are not seen at the C-term in both molecules.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,7694
Polymers59,3792
Non-polymers3902
Water11,944663
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8852
Polymers29,6891
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8852
Polymers29,6891
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.65, 66.15, 134.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BETA-LACTAMASE / / CEPHALOSPORINASE


Mass: 29689.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Strain: K1 / Gene: BLAC / Plasmid: PPVCF1 / Production host: Escherichia coli (E. coli) / Strain (production host): AS226-51 / References: UniProt: P52664, beta-lactamase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: PEG 6000, MES, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 44.1 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
212.5 %(w/v)PEG60001drop
312.5 mMMES1droppH6.25
425 %PEG1reservoir
525 mMMES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 3, 1999 / Details: Franks mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.75→44 Å / Num. all: 53765 / Num. obs: 49364 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.76 % / Biso Wilson estimate: 24 Å2 / Rsym value: 5.2 / Net I/σ(I): 18.5
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 5658 / Rsym value: 20.3 / % possible all: 64.6
Reflection
*PLUS
% possible obs: 92 % / Num. measured all: 284238 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 65 % / Num. unique obs: 5658 / Num. measured obs: 15124 / Rmerge(I) obs: 0.2

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BZA

1bza


Resolution: 1.75→44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 999 -RANDOM
Rwork0.169 ---
all-48685 --
obs-48685 91.5 %-
Solvent computationSolvent model: flat model / Bsol: 42.2 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 13.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.75→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 48 663 4779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_bond_d0.0045
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection% reflection
Rfree0.267 41 -
Rwork0.239 --
obs-2539 49 %
Refinement
*PLUS
Rfactor obs: 0.169 / Rfactor Rfree: 0.193 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_plane_restr0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.267 / Rfactor Rwork: 0.239 / Num. reflection obs: 2580 / Rfactor obs: 0.239

+
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