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- PDB-5h6g: Crystal structure of a thermostable lipase from Marine Streptomyces -

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Basic information

Entry
Database: PDB / ID: 5h6g
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 / metal ion binding / : / PHOSPHATE ION / Putative secreted lipase
Function and homology information
Biological speciesStreptomyces sp. W007 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
Revision 1.3Nov 8, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted lipase
B: Putative secreted lipase
C: Putative secreted lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,25411
Polymers86,6723
Non-polymers5828
Water1,982110
1
A: Putative secreted lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0574
Polymers28,8911
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10460 Å2
MethodPISA
2
B: Putative secreted lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2155
Polymers28,8911
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-6 kcal/mol
Surface area10600 Å2
MethodPISA
3
C: Putative secreted lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9832
Polymers28,8911
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.500, 129.500, 137.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

CL

21A-303-

CL

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Putative secreted lipase


Mass: 28890.670 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 118 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.85 Å3/Da / Density % sol: 68.05 % / Mosaicity: 0.44 °
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.0M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.34→64.75 Å / Num. obs: 56185 / % possible obs: 99.2 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.032 / Rrim(I) all: 0.104 / Net I/σ(I): 15.4 / Num. measured all: 590046 / Scaling rejects: 860
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.34-2.4110.40.9294704045330.8210.30.9771.798.8
9.93-64.759.30.03776668220.9970.0130.03948.599.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.1.30data scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H6B

5h6b


Resolution: 2.34→64.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.237 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 2850 5.1 %RANDOM
Rwork0.1914 ---
obs0.1929 53333 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.59 Å2 / Biso mean: 42.999 Å2 / Biso min: 24.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å2-0 Å2
3----1.51 Å2
Refinement stepCycle: final / Resolution: 2.34→64.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 29 110 5870
Biso mean--82.55 35.61 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195912
X-RAY DIFFRACTIONr_bond_other_d0.0020.025570
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9688096
X-RAY DIFFRACTIONr_angle_other_deg1.003312824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30124.16238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48915850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7271524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021310
X-RAY DIFFRACTIONr_mcbond_it2.4024.1683037
X-RAY DIFFRACTIONr_mcbond_other2.4014.1673036
X-RAY DIFFRACTIONr_mcangle_it3.7096.2413791
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 207 -
Rwork0.293 3885 -
all-4092 -
obs--98.72 %

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