[English] 日本語
Yorodumi
- PDB-1alq: CIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1alq
TitleCIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1
ComponentsCP254 BETA-LACTAMASE
KeywordsHYDROLASE / CIRCULAR PERMUTED / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / 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 ...Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Beta-lactamase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å
AuthorsPieper, U. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 1997
Title: Circularly permuted beta-lactamase from Staphylococcus aureus PC1.
Authors: Pieper, U. / Hayakawa, K. / Li, Z. / Herzberg, O.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 A Resolution
Authors: Herzberg, O.
#2: Journal: Science / Year: 1987
Title: Bacterial Resistance to Beta-Lactam Antibiotics: Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 A Resolution
Authors: Herzberg, O. / Moult, J.
History
DepositionJun 2, 1997Processing site: BNL
Revision 1.0Sep 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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: CP254 BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8023
Polymers29,6461
Non-polymers1562
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.900, 94.200, 138.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21A-386-

HOH

31A-388-

HOH

-
Components

#1: Protein CP254 BETA-LACTAMASE


Mass: 29646.125 Da / Num. of mol.: 1
Mutation: CIRCULARLY PERMUTED WITH AN EIGHT RESIDUE LINKER INSERTED TO JOIN THE ORIGINAL N- AND C-TERMINI, AND A NEW N-TERMINUS AT RESIDUE 254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00807, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.96 Å3/Da / Density % sol: 57 %
Description: RESIDUES 31 - 34, 252 - 256, 288 - 290 AND THE SOLVENT WERE EXCLUDED FROM THE STARTING MODEL.
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 70% SATURATED AMMONIUM SULFATE SOLUTION, 0.3M KCL, 100MM NAHCO3 AT PH8.0, 0.5% V/V PEG600
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
230 %satammonium sulfate1drop
35 mMpotassium phosphate1drop
435 %satammonium sulfate1drop
50.15 M1dropKCl
650 mM1dropNaHCO3
70.25 %(v/v)PEG60001drop
870 %satammonium sulfate1reservoir
90.3 M1reservoirKCl
10100 mM1reservoirNaHCO3
110.5 %(v/v)PEG60001reservoir

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 29813 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.8 / % possible all: 66
Reflection
*PLUS
Num. measured all: 147535

-
Processing

Software
NameVersionClassification
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
XENGENV. 3.0data reduction
XENGENV. 3.0data scaling
SHELXL-97phasing
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 3BLM

3blm


Resolution: 1.8→30 Å / Num. parameters: 9029 / Num. restraintsaints: 8373 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.9 ANGSTROMS. AT R-VALUES OF R=0.189 AND RFREE=0.241 FOR ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.9 ANGSTROMS. AT R-VALUES OF R=0.189 AND RFREE=0.241 FOR I>I/SIGMA(I) THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2981 10 %EVERY 10TH REFLECTION
all0.196 29777 --
obs0.191 -88.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2122 / Occupancy sum non hydrogen: 2203.5
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 9 212 2254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.118
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.082
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.034

+
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