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- PDB-1qge: NEW CRYSTAL FORM OF PSEUDOMONAS GLUMAE (FORMERLY CHROMOBACTERIUM ... -

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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 / triglyceride 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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: EXTRACELLULARGlossary of biology / 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: EXTRACELLULARGlossary of biology / 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 / 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
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).

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Experimental details

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Experiment

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

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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

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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

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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

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