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- PDB-1vjg: Crystal structure of a gdsl-like lipase (alr1529) from nostoc sp.... -

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Basic information

Entry
Database: PDB / ID: 1vjg
TitleCrystal structure of a gdsl-like lipase (alr1529) from nostoc sp. pcc 7120 at 2.01 A resolution
Componentsputative lipase from the G-D-S-L family
KeywordsHYDROLASE / Putative lipase from the g-d-s-l family / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Alr1529 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative lipase from the G-D-S-L family from Nostoc sp. at 2.01 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative lipase from the G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)25,1331
Polymers25,1331
Non-polymers00
Water1,65792
1
A: putative lipase from the G-D-S-L family

A: putative lipase from the G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)50,2672
Polymers50,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Unit cell
Length a, b, c (Å)56.192, 56.192, 129.318
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein putative lipase from the G-D-S-L family


Mass: 25133.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: ALR1529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YWS4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 10% iso-propanol, 20% PEG-4000, 0.1M Sodium HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9801
DetectorType: ADSC / Detector: CCD / Date: Jul 13, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.01→43.32 Å / Num. obs: 15039 / % possible obs: 90.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 57.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1526 / Rsym value: 0.277 / % possible all: 65.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→43.32 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.678 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21832 749 5 %RANDOM
Rwork0.17247 ---
obs0.17454 14261 90.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20.99 Å20 Å2
2--1.98 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.01→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 0 92 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211685
X-RAY DIFFRACTIONr_bond_other_d0.0020.021513
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9352302
X-RAY DIFFRACTIONr_angle_other_deg0.88233518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375210
X-RAY DIFFRACTIONr_chiral_restr0.0910.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined0.210.2314
X-RAY DIFFRACTIONr_nbd_other0.2390.21679
X-RAY DIFFRACTIONr_nbtor_other0.0850.2968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.24
X-RAY DIFFRACTIONr_mcbond_it2.04431017
X-RAY DIFFRACTIONr_mcangle_it3.64951658
X-RAY DIFFRACTIONr_scbond_it5.8268668
X-RAY DIFFRACTIONr_scangle_it8.611639
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 39 5.23 %
Rwork0.203 706 -
Refinement TLS params.Method: refined / Origin x: 1.66 Å / Origin y: 36.085 Å / Origin z: 16.352 Å
111213212223313233
T0.0397 Å20.0169 Å2-0.0072 Å2-0.1226 Å20.0083 Å2--0.0042 Å2
L0.7576 °2-0.1702 °20.2178 °2-1.4352 °20.7349 °2--2.7323 °2
S0.062 Å °-0.0223 Å °-0.1029 Å °0.0162 Å °-0.1153 Å °0.0556 Å °0.3057 Å °0.0022 Å °0.0533 Å °
Refinement TLS groupSelection: ALL

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