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- PDB-7q4j: A thermostable lipase from Thermoanaerobacter thermohydrosulfuric... -

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Basic information

Entry
Database: PDB / ID: 7q4j
TitleA thermostable lipase from Thermoanaerobacter thermohydrosulfuricus in complex a monoacylglycerol intermediate
Components(Serine aminopeptidase S33 domain-containing ...) x 2
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / THERMOSTABLE / monoacylglycerol / lipase
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / DECANE / nonane / N-OCTANE / STEARIC ACID / Serine aminopeptidase S33 domain-containing protein
Function and homology information
Biological speciesThermoanaerobacter thermohydrosulfuricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsPinotsis, N. / Wilmanns, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A thermostable lipase from Thermoanaerobacter thermohydrosulfuricus in complex a monoacylglycerol intermediate
Authors: Pinotsis, N. / Wilmanns, M.
History
DepositionOct 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / pdbx_molecule_features / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine aminopeptidase S33 domain-containing protein
B: Serine aminopeptidase S33 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13420
Polymers60,0022
Non-polymers2,13218
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The mutation E72R abolishes the dimerisation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-29 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.526, 137.526, 67.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Serine aminopeptidase S33 domain-containing ... , 2 types, 2 molecules AB

#1: Protein Serine aminopeptidase S33 domain-containing protein / Prolyl oligopeptidase family


Mass: 29960.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Methylates Lysines, Seleno-methionines
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: SAMN04244560_02687 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7VV58
#2: Protein Serine aminopeptidase S33 domain-containing protein


Mass: 30040.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: SAMN04244560_02687 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7VV58

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Non-polymers , 8 types, 305 molecules

#3: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-DD9 / nonane / Nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#9: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.26 % / Description: parallelepiped of about 50 x 50 x 100 micro-m
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.4 M ammonium sulfate, 0.1 M TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97873, 0.97903
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978731
20.979031
ReflectionResolution: 1.91→20 Å / Num. obs: 49383 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.26 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.4
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2071 / CC1/2: 0.99 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→19.75 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1939 1532 3.11 %
Rwork0.1631 47663 -
obs0.164 49195 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 1.91→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 136 287 4558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434385
X-RAY DIFFRACTIONf_angle_d0.83335856
X-RAY DIFFRACTIONf_chiral_restr0.047633
X-RAY DIFFRACTIONf_plane_restr0.006732
X-RAY DIFFRACTIONf_dihedral_angle_d15.19791687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.970.2199960.25363803X-RAY DIFFRACTION85.96
1.97-2.040.26071470.20874291X-RAY DIFFRACTION97.35
2.04-2.120.23391410.18854310X-RAY DIFFRACTION97.67
2.12-2.220.25121250.16954334X-RAY DIFFRACTION97.89
2.22-2.340.19231540.16474344X-RAY DIFFRACTION98.34
2.34-2.480.21191380.17734373X-RAY DIFFRACTION98.77
2.48-2.670.21541380.17944390X-RAY DIFFRACTION98.5
2.67-2.940.20161560.18524408X-RAY DIFFRACTION98.47
2.94-3.370.22961530.1834386X-RAY DIFFRACTION98.03
3.37-4.230.17531520.14354425X-RAY DIFFRACTION97.3
4.24-19.750.15371320.14074599X-RAY DIFFRACTION96.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.10756536479-0.3006813262070.1747840800461.74849102090.1122912830231.4023695721-0.05593959334320.00886421425176-0.500929692958-0.02372523235440.0150980117030.1468556151650.117326728787-0.2826258697280.03853652511820.270285550576-0.04394798619250.04401674101060.402318396889-0.02821614795630.4254184252231.6599904574229.85465742464.50445955336
24.323224656731.652827742850.07197299580691.91455563837-0.5322997265080.976546422788-0.1669873925180.3582925289390.320476010412-0.3171068198630.1500218252350.152716329262-0.216659912162-0.323968378236-0.01117193220720.4371773008730.01767514384990.009477487557960.462777423451-0.001094083105270.34139625194810.119743944748.6357309495-8.37299139125
31.706880378630.181024411285-0.02069781107772.382353762920.3757924083341.57515042741-0.0528303318663-0.140718453031-0.2268103178520.1008471802070.0577279700913-0.314138830387-0.04285034258130.146345861159-0.002140968720990.2569125392440.00573608480355-0.014372214430.3445482933890.06120230460130.33215558717327.802473838441.766960192718.831591889
43.09791000350.768959336364-0.7790990749621.45844098780.6417232567280.7761867494840.0609148501649-0.4872131334660.05309144919280.306267530358-0.07353767196110.16498120502-0.0808108995950.02681312062710.02284277738690.3959080417080.01848407421550.02314171690320.4753151048450.07756415979570.3057721140637.8908928018648.016363355531.6032867597
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resid 1:140 or resid 183:259)AA1 - 2591 - 259
22chain A and resid 141:182AA141 - 182141 - 182
33chain B and (resid 1:140 or resid 183:259)BB1 - 2591 - 259
44chain B and resid 141:182BB141 - 182141 - 182

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