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- PDB-4lhs: Crystal structure of a putative GDSL-like lipase (BACOVA_00914) f... -

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Basic information

Entry
Database: PDB / ID: 4lhs
TitleCrystal structure of a putative GDSL-like lipase (BACOVA_00914) from Bacteroides ovatus ATCC 8483 at 1.40 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domains protein / N-terminus GxDLY domain (PF14607 family) / C-terminus lipase GDSL 3 (PF14606 family) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


SGNH hydrolase-type esterase, N-terminal / GDSL-like Lipase/Acylhydrolase family / N-terminus of Esterase_SGNH_hydro-type / SGNH hydrolase / SGNH hydrolase-type esterase domain / SGNH hydrolase superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich ...SGNH hydrolase-type esterase, N-terminal / GDSL-like Lipase/Acylhydrolase family / N-terminus of Esterase_SGNH_hydro-type / SGNH hydrolase / SGNH hydrolase-type esterase domain / SGNH hydrolase superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_00914) from Bacteroides ovatus ATCC 8483 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1334
Polymers38,8281
Non-polymers3043
Water6,648369
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2658
Polymers77,6562
Non-polymers6096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5200 Å2
ΔGint2 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.890, 71.573, 63.102
Angle α, β, γ (deg.)90.000, 125.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

GOL

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Components

#1: Protein Uncharacterized protein


Mass: 38828.242 Da / Num. of mol.: 1 / Fragment: UNP residues 23-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_00914 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LSX5
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 24-365) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 24-365) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.0500M lithium sulfate, 10.00% Glycerol, 30.00% polyethylene glycol 600, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 14, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.4→29.317 Å / Num. obs: 61438 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.95 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.87
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.450.61822966412167198.9
1.45-1.510.4562.83110012545199.4
1.51-1.580.3293.73121412498199.5
1.58-1.660.2374.82957211743199.6
1.66-1.760.1746.12986911858199.6
1.76-1.90.1188.13181412628199.2
1.9-2.090.07511.52990512083198.6
2.09-2.390.05714.22963712023198
2.39-3.010.04516.62964212029196.9
3.01-29.3170.034202840111434191.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→29.317 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 1.8 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.055
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.GLYCEROL (GOL) AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1637 3096 5 %RANDOM
Rwork0.1261 ---
obs0.128 61401 98.62 %-
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 max: 52.89 Å2 / Biso mean: 16.3098 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.02 Å2
2--0.59 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 20 369 3033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222929
X-RAY DIFFRACTIONr_bond_other_d0.0020.022091
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9874000
X-RAY DIFFRACTIONr_angle_other_deg1.07535181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29824.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28515576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5381518
X-RAY DIFFRACTIONr_chiral_restr0.0970.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213237
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02559
X-RAY DIFFRACTIONr_mcbond_it2.35231786
X-RAY DIFFRACTIONr_mcbond_other1.3663715
X-RAY DIFFRACTIONr_mcangle_it3.27752946
X-RAY DIFFRACTIONr_scbond_it4.57481143
X-RAY DIFFRACTIONr_scangle_it6.793111018
X-RAY DIFFRACTIONr_rigid_bond_restr1.71435020
X-RAY DIFFRACTIONr_sphericity_free7.2133376
X-RAY DIFFRACTIONr_sphericity_bonded3.6734936
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 239 -
Rwork0.208 4307 -
all-4546 -
obs--99.32 %

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