[English] 日本語
Yorodumi
- PDB-1isp: Crystal structure of Bacillus subtilis lipase at 1.3A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1isp
TitleCrystal structure of Bacillus subtilis lipase at 1.3A resolution
Componentslipase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsKawasaki, K. / Kondo, H. / Suzuki, M. / Ohgiya, S. / Tsuda, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3 A resolution.
Authors: Kawasaki, K. / Kondo, H. / Suzuki, M. / Ohgiya, S. / Tsuda, S.
History
DepositionDec 19, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4752
Polymers19,3831
Non-polymers921
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.200, 58.450, 82.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein lipase /


Mass: 19382.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: pWSL1 / Production host: Bacillus megaterium (bacteria) / Strain (production host): WH320 / References: UniProt: P37957, triacylglycerol lipase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: PEG 8000, glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.7-8.8
26-9 %(w/v)PEG80001reservoir
317 %(v/v)glycerol1reservoir
420 mMTris-HCl1droppH7.5
515 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Nov 7, 2000 / Details: BENT PLANE FUSED QUARTZ
RadiationMonochromator: Bent Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 44447 / Num. obs: 44447 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 6.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5209 / % possible all: 79.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 169453
Reflection shell
*PLUS
% possible obs: 79.9 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1330 2.992 %RANDOM
Rwork0.192 ---
all-44447 --
obs-44447 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 6 151 1508
Refine LS restraintsType: s_bond_d / Dev ideal: 0.029
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.36
LS refinement shell
*PLUS
Rfactor Rwork: 0.265

+
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