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- PDB-5h6b: Crystal structure of a thermostable lipase from Marine Streptomyces -

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Basic information

Entry
Database: PDB / ID: 5h6b
TitleCrystal structure of a thermostable lipase from Marine Streptomyces
ComponentsPutative secreted lipase
KeywordsHYDROLASE / Lipase / Thermostability / Marine
Function / homologyLipase EstA/Esterase EstB / Lipase (class 2) / lipid catabolic process / Alpha/Beta hydrolase fold / hydrolase activity / ACETATE ION / IMIDAZOLE / Putative secreted lipase
Function and homology information
Biological speciesStreptomyces sp. W007 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHou, S. / Zhao, Z. / Liu, J.
CitationJournal: FEBS J. / Year: 2017
Title: Crystal structure of a lipase from Streptomyces sp. strain W007 - implications for thermostability and regiospecificity
Authors: Zhao, Z. / Hou, S. / Lan, D. / Wang, X. / Liu, J. / Khan, F.I. / Wang, Y.
History
DepositionNov 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5809
Polymers28,0621
Non-polymers5188
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-118 kcal/mol
Surface area10290 Å2
2
A: Putative secreted lipase
hetero molecules

A: Putative secreted lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,15918
Polymers56,1242
Non-polymers1,03616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area3060 Å2
ΔGint-103 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.730, 90.730, 70.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Putative secreted lipase


Mass: 28061.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. W007 (bacteria) / Strain: W007 / Gene: SPW_1544 / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: H0B8D4, triacylglycerol lipase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.99 Å3/Da / Density % sol: 58.86 % / Mosaicity: 0.49 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.2M Zn(AC)2, 0.1M imidazole, pH 6.5, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2822 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.3→70.63 Å / Num. obs: 14806 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.718 / Num. measured obs: 15663 / Num. unique all: 1433 / CC1/2: 0.903 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata collection
Aimless0.5.15data scaling
PHASESphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→70.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.781 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 827 5.6 %RANDOM
Rwork0.178 ---
obs0.1796 13955 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.29 Å2 / Biso mean: 45.597 Å2 / Biso min: 29.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.56 Å2-0 Å2
2---1.11 Å20 Å2
3---3.62 Å2
Refinement stepCycle: final / Resolution: 2.3→70.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 22 45 1970
Biso mean--55.14 47.27 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191972
X-RAY DIFFRACTIONr_bond_other_d0.0020.021865
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9722695
X-RAY DIFFRACTIONr_angle_other_deg0.96834289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13224.17779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36515283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.106158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212250
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
X-RAY DIFFRACTIONr_mcbond_it2.2014.4591009
X-RAY DIFFRACTIONr_mcbond_other2.1964.4521006
X-RAY DIFFRACTIONr_mcangle_it3.2586.6721257
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 54 -
Rwork0.264 1036 -
all-1090 -
obs--100 %

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