[English] 日本語
Yorodumi
- PDB-1qge: NEW CRYSTAL FORM OF PSEUDOMONAS GLUMAE (FORMERLY CHROMOBACTERIUM ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qge
TitleNEW CRYSTAL FORM OF PSEUDOMONAS GLUMAE (FORMERLY CHROMOBACTERIUM VISCOSUM ATCC 6918) LIPASE
Components(PROTEIN (TRIACYLGLYCEROL HYDROLASE)) x 2
KeywordsHYDROLASE / PSEUDOMONADACEAE / CIS-PEPTIDE / CLOSED CONFORMATION / LID
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
Lipases, serine active site. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Triacylglycerol lipase / Triacylglycerol lipase
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLang, D.A. / Stadler, P. / Kovacs, A. / Paltauf, F. / Dijkstra, B.W.
Citation
Journal: To be Published
Title: Structural and Kinetic Investigations of Enantiomeric Binding Mode of Subclass I Lipases from the Family of Pseudomonadaceae
Authors: Lang, D.A. / Stadler, P. / Kovacs, A. / Paltauf, F. / Dijkstra, B.W.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6 angstroms resolution.
Authors: Lang, D. / Hofmann, B. / Haalck, L. / Hecht, H.J. / Spener, F. / Schmid, R.D. / Schomburg, D.
#2: Journal: Febs Lett. / Year: 1993
Title: The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate.
Authors: Noble, M.E. / Cleasby, A. / Johnson, L.N. / Egmond, M.R. / Frenken, L.G.
History
DepositionApr 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 16, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: PROTEIN (TRIACYLGLYCEROL HYDROLASE)
E: PROTEIN (TRIACYLGLYCEROL HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1743
Polymers33,1342
Non-polymers401
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-64 kcal/mol
Surface area12490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.980, 43.350, 140.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (TRIACYLGLYCEROL HYDROLASE) / EC 3.1.1.3


Mass: 22954.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATCC / Source: (natural) Burkholderia glumae (bacteria) / Cellular location: EXTRACELLULAR / Strain: CHROMOBACTERIUM VISCOSUM
References: UniProt: Q05489, UniProt: P0DUB9*PLUS, triacylglycerol lipase
#2: Protein PROTEIN (TRIACYLGLYCEROL HYDROLASE) / EC 3.1.1.3


Mass: 10179.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATCC / Source: (natural) Burkholderia glumae (bacteria) / Cellular location: EXTRACELLULAR / Strain: CHROMOBACTERIUM VISCOSUM
References: UniProt: Q05489, UniProt: P0DUB9*PLUS, triacylglycerol lipase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC PROTEOLYTIC DIGESTION DURING PURIFICATION AND/OR ...PARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC PROTEOLYTIC DIGESTION DURING PURIFICATION AND/OR STORAGE PROVEN BY MALDI-TOF MASS SPECTROSCOPY MOLECULAR WEIGHT: CALCULATED -- 33091 DALTON, MEASURED -- 32839 DALTON NO OXYANION LOOP FORMATION, BUT A SLIGHT MOVEMENT OF THE LID REGION ALREADY OCCURED. THE STRUCTURE STILL REPRESENTS THE CLOSED, INACTIVE CONFORMATIONAL STATES OF THE LIPASE
Has protein modificationY
Sequence details1QGE SWS Q05489 1 - 39 NOT IN ATOMS LIST REFERENCE: THE SEQUENCE FOR PSEUDOMONAS GLUMAE DESCRIBED ...1QGE SWS Q05489 1 - 39 NOT IN ATOMS LIST REFERENCE: THE SEQUENCE FOR PSEUDOMONAS GLUMAE DESCRIBED IN FRENKEN ET AL. (1992), APPL. ENVIR. MICROBIOL. 58 3787-3791; IS IDENTICAL TO THE AMINO ACID SEQUENCE OF CHROMOBACTERIUM VISCOSUM DESCRIBED IN SHIZUOKA ET AL., 1989 (GERMAN PATENT 3908131 A1).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 7.8
Details: PROTEIN WAS CRYSTALLIZED FROM 10 % PEG 6000, 5 % PEG 1000, 100 MM HEPES BUFFER, PH 7.8

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 28124 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.067 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.27 / % possible all: 94.4

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CVL

1cvl


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE DISORDERED REGION (VAL 220, LEU 221 AND GLY 223) WAS NOT MODELED OR REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1410 5 %RANDOM
Rwork0.187 ---
obs0.213 28058 98.6 %-
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 1 324 2640
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9592
X-RAY DIFFRACTIONp_mcangle_it1.4953
X-RAY DIFFRACTIONp_scbond_it1.1932
X-RAY DIFFRACTIONp_scangle_it1.8173
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1040.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor12.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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