[English] 日本語
Yorodumi
- PDB-1r50: Bacillus subtilis lipase A with covalently bound Sc-IPG-phosphona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r50
TitleBacillus subtilis lipase A with covalently bound Sc-IPG-phosphonate-inhibitor
ComponentsLipase
KeywordsHYDROLASE / lipase / alpha/beta hydrolase / phosphonate inhibitor
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triacylglycerol 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
Chem-SIL / Lipase EstA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDroege, M.J. / Van Pouderoyen, G. / Vrenken, T.E. / Rueggeberg, C.J. / Reetz, M.T. / Dijkstra, B.W. / Quax, W.J.
CitationJournal: Chembiochem / Year: 2005
Title: Directed Evolution of Bacillus subtilis Lipase A by Use of Enantiomeric Phosphonate Inhibitors: Crystal Structures and Phage Display Selection
Authors: Droege, M.J. / Boersma, Y.L. / van Pouderoyen, G. / Vrenken, T.E. / Rueggeberg, C.J. / Reetz, M.T. / Dijkstra, B.W. / Quax, W.J.
History
DepositionOct 9, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3224
Polymers38,7662
Non-polymers5572
Water4,414245
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6612
Polymers19,3831
Non-polymers2781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6612
Polymers19,3831
Non-polymers2781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.594, 83.591, 95.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Lipase / lipase A


Mass: 19382.836 Da / Num. of mol.: 2 / Fragment: residues 1-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: PMA5LIP / Production host: Bacillus subtilis (bacteria) / Strain (production host): BCL1051 / References: UniProt: P37957, triacylglycerol lipase
#2: Chemical ChemComp-SIL / [(4S)-2,2-DIMETHYL-1,3-DIOXOLAN-4-YL]METHYL HYDROGEN HEX-5-ENYLPHOSPHONATE / O-[(S)-1,2-O-ISOPROPYLIDENE-SN-GLYCEROL]6-HEXENYL PHOSPHONATE / O-[(S)-IPG] 6-HEXENYL PHOSPHONATE


Mass: 278.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H23O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 1.89 Å3/Da / Density % sol: 34.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10
Details: PEG 4000, ETHANOL AMINE, SODIUM SULPHATE, CADMIUM CHLORIDE, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2001 / Details: MIRRORS
RadiationMonochromator: SI111 OR SI311 CRYSTALS, LN2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. all: 56823 / Num. obs: 48857 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.042 / Net I/σ(I): 27.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1001 / Rsym value: 0.305 / % possible all: 35.4

-
Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bacillus subtilis lipase A

Resolution: 1.45→100 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2467 5 %RANDOM
Rwork0.196 ---
all-56823 --
obs-48747 85.8 %-
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-0.722 Å20 Å20 Å2
2---0.857 Å20 Å2
3---0.135 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 1.45→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 34 245 2981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004685
X-RAY DIFFRACTIONc_angle_deg1.22808

+
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