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- PDB-2lip: PSEUDOMONAS LIPASE OPEN CONFORMATION -

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Basic information

Entry
Database: PDB / ID: 2lip
TitlePSEUDOMONAS LIPASE OPEN CONFORMATION
ComponentsLIPASE
KeywordsHYDROLASE / LIPASE / PSEUDOMONAS / CATALYTIC TRIAD
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
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchrag, J.D. / Cygler, M.
CitationJournal: Structure / Year: 1997
Title: The open conformation of a Pseudomonas lipase.
Authors: Schrag, J.D. / Li, Y. / Cygler, M. / Lang, D. / Burgdorf, T. / Hecht, H.J. / Schmid, R. / Schomburg, D. / Rydel, T.J. / Oliver, J.D. / Strickland, L.C. / Dunaway, C.M. / Larson, S.B. / Day, J. / McPherson, A.
History
DepositionDec 13, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1912
Polymers33,1511
Non-polymers401
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.500, 47.340, 85.220
Angle α, β, γ (deg.)90.00, 121.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LIPASE / TRIACYLGLYCEROL HYDROLASE


Mass: 33150.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMMERCIAL PREP FROM GENZYME CORPORATION / Source: (natural) Burkholderia cepacia (bacteria) / References: UniProt: P22088, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 50% N-PROPANOL, 50 MM TRIS, PH 8.5, 291 K, HANGING DROP VAPOR DIFFUSION, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 %n-propanol1reservoir
250 mMTris-HCl1reservoirpH8.5
316-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 23, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→39.11 Å / Num. obs: 14497 / % possible obs: 79.4 % / Observed criterion σ(I): 1 / Redundancy: 1.69 % / Rsym value: 0.0603 / Net I/σ(I): 9.12
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.96 / % possible all: 60.6
Reflection
*PLUS
Num. measured all: 24516 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
RAXISII(MSC)data collection
RAXISII(MSC)data reduction
X-PLORmodel building
X-PLORrefinement
R-AXISII (MSC)data reduction
R-AXIS(MSC)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TAH

1tah


Resolution: 2.1→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 999999 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: DENSITY FOR RESIDUES 19 - 27 IS FRAGMENTED AND POSITIONS ARE UNCERTAIN. MODELED POSITIONS ARE BEST GUESS. THE OCCUPANCIES WERE SET TO 0.2 INDICATE THE UNCERTAINTY. LYS 22 SEEMED CLEARER AND ...Details: DENSITY FOR RESIDUES 19 - 27 IS FRAGMENTED AND POSITIONS ARE UNCERTAIN. MODELED POSITIONS ARE BEST GUESS. THE OCCUPANCIES WERE SET TO 0.2 INDICATE THE UNCERTAINTY. LYS 22 SEEMED CLEARER AND ITS SIDE CHAIN WAS INCLUDED, BUT STILL SHOULD BE REGARDED AS A GUESS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1281 10 %RANDOM
Rwork0.163 ---
obs0.163 12694 --
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 1 91 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.247 95
Rwork0.208 924
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCDSX.PROTOPHCDSX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM_CIS.PROTOPH_CIS.PRO
X-RAY DIFFRACTION4PARAM19.IONTOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.175 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23

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