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- PDB-7q4h: A thermostable lipase from Thermoanaerobacter thermohydrosulfuric... -

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Basic information

Entry
Database: PDB / ID: 7q4h
TitleA thermostable lipase from Thermoanaerobacter thermohydrosulfuricus in complex with PMSF
Components(Hydrolase_4 domain-containing ...) x 2
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / THERMOSTABLE / PMSF
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / :
Function and homology information
Biological speciesThermoanaerobacter thermohydrosulfuricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00003223771 Å
AuthorsPinotsis, N. / Wilmanns, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex.
Authors: Pinotsis, N. / Kruger, A. / Tomas, N. / Chatziefthymiou, S.D. / Litz, C. / Mortensen, S.A. / Daffe, M. / Marrakchi, H. / Antranikian, G. / Wilmanns, M.
History
DepositionOct 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase_4 domain-containing protein
B: Hydrolase_4 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,00411
Polymers58,9562
Non-polymers1,0499
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The mutation E72R abolishes the dimerisation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-54 kcal/mol
Surface area20130 Å2
Unit cell
Length a, b, c (Å)84.808, 84.808, 157.484
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

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Hydrolase 4 domain-containing ... , 2 types, 2 molecules AB

#1: Protein Hydrolase_4 domain-containing protein


Mass: 29450.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Methylated lysines
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: SAMN04324257_00243 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I1X7Z7
#2: Protein Hydrolase_4 domain-containing protein


Mass: 29504.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: SAMN04324257_00243 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I1X7Z7

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Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.43 Å3/Da / Density % sol: 49.36 % / Description: long, very thin rods
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 2.4M Ammonium Sulfate, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 38930 / % possible obs: 98.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 37.3789775577 Å2 / CC1/2: 0.99 / Rsym value: 0.082 / Net I/σ(I): 24
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2422 / CC1/2: 0.99 / Rsym value: 0.514

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure

Resolution: 2.00003223771→29.9841559494 Å / SU ML: 0.268164055868 / Cross valid method: FREE R-VALUE / σ(F): 1.40023011694 / Phase error: 25.2434670547
RfactorNum. reflection% reflection
Rfree0.228000812825 1219 3.13359553739 %
Rwork0.184258466292 37682 -
obs0.18567197857 38901 98.1555308841 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.002510335 Å2
Refinement stepCycle: LAST / Resolution: 2.00003223771→29.9841559494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 0 65 136 4302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004617168173374260
X-RAY DIFFRACTIONf_angle_d0.9374255002585712
X-RAY DIFFRACTIONf_chiral_restr0.0347405243805621
X-RAY DIFFRACTIONf_plane_restr0.00287955494721
X-RAY DIFFRACTIONf_dihedral_angle_d16.2494872991602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.08010.3513431769491340.3149388128453616X-RAY DIFFRACTION86.8860055607
2.0801-2.17470.3516483642661240.2713904515794153X-RAY DIFFRACTION98.18640955
2.1747-2.28940.2762134276491190.2327308796814160X-RAY DIFFRACTION99.650675361
2.2894-2.43270.2917655873621340.2165014244234200X-RAY DIFFRACTION99.7009431792
2.4327-2.62050.2324386534391340.2005793129744197X-RAY DIFFRACTION99.7466605251
2.6205-2.8840.26554167261280.1990900461424249X-RAY DIFFRACTION99.6357842021
2.884-3.30080.2605447113851570.2013903257454252X-RAY DIFFRACTION99.8188815938
3.3008-4.15690.2023060135811480.1612564381894302X-RAY DIFFRACTION99.6640537514
4.1569-29.9840.1782937199281410.1498620490154553X-RAY DIFFRACTION99.8298596342
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)
11.00279256383-0.0480970563235-0.05669518448510.923150479194-0.1282477869710.822401364718-0.08408113548580.04440327553150.317447639113-0.01828840137340.05996766891690.133651494082-0.2745707274760.3574635326160.02608353538480.22702741255-0.0908069732974-0.01796736133730.3328114562240.0002660757568870.31453318383920.0791449269-14.94363887063.34399289802
21.082287938410.2397664254720.4778659158561.74530223268-0.3749909513820.6342594152190.151023288908-0.512400544968-0.1441326187350.403800189014-0.0005150106366840.2704148364030.1239688317380.04342787580960.2658050430670.231075808429-0.004678157873710.04927446165930.3547665280360.0768020003040.27328392383611.0688697936-41.377318744218.6543774732
30.7472234814841.036197188450.4639106573462.80726956742-0.146698539861.39348687955-0.1257230782180.309117554721-0.125560375674-0.6488448637890.190222986843-0.3971751913210.3665288176640.697243258616-0.04245013221560.3950075990230.03637350131280.04122238317250.608235457585-0.03279798820060.28063650719126.2188346842-34.132719141-9.83388786763
40.148731266058-0.006695352903830.0002600440838810.1265061678550.03699789640730.01155676664480.288487580956-0.233150185056-0.005019659708080.386227660394-0.0419556206655-0.3052609603440.007569640389670.0001613406067180.0008454767603230.492571244471-0.0696508106571-0.04759702011990.661037523136-0.03616135412040.30402303696429.3914232846-31.218950689430.7205566576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:140) or (resseq 183:259))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:140) or (resseq 183:259))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 141:182))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 141:182))

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