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- PDB-8b9s: NATIVE FORM, THERMOSTABLE LIPASE FROM THERMOANAEROBACTER THERMOHY... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8b9s
TitleNATIVE FORM, THERMOSTABLE LIPASE FROM THERMOANAEROBACTER THERMOHYDROSULFURICUS
ComponentsProlyl oligopeptidase family protein
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / THERMOSTABLE
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / DECANE / : / PHOSPHATE ION / Prolyl oligopeptidase family protein
Function and homology information
Biological speciesThermoanaerobacter thermohydrosulfuricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 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: Prolyl oligopeptidase family protein
B: Prolyl oligopeptidase family protein
C: Prolyl oligopeptidase family protein
D: Prolyl oligopeptidase family protein
E: Prolyl oligopeptidase family protein
F: Prolyl oligopeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,33818
Polymers175,2216
Non-polymers1,11712
Water6,125340
1
A: Prolyl oligopeptidase family protein
B: Prolyl oligopeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9247
Polymers58,4072
Non-polymers5165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Prolyl oligopeptidase family protein
D: Prolyl oligopeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5944
Polymers58,4072
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Prolyl oligopeptidase family protein
F: Prolyl oligopeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8207
Polymers58,4072
Non-polymers4135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.237, 125.237, 101.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 2 or (resid 3...
d_2ens_1(chain "B" and (resid 1 through 2 or (resid 3...
d_3ens_1(chain "C" and (resid 1 through 2 or (resid 3...
d_4ens_1(chain "D" and (resid 1 through 2 or (resid 3...
d_5ens_1(chain "E" and (resid 1 through 55 or resid 57...
d_6ens_1(chain "F" and (resid 1 through 2 or (resid 3...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETLEULEUAA1 - 551 - 55
d_12LYSLYSGLYGLYAA57 - 7557 - 75
d_13PHEPHELEULEUAA77 - 11277 - 112
d_14METMETMETMETAA114 - 158114 - 158
d_15GLNGLNGLYGLYAA160 - 259160 - 259
d_21METMETLEULEUBB1 - 551 - 55
d_22LYSLYSGLYGLYBB57 - 7557 - 75
d_23PHEPHELEULEUBB77 - 11277 - 112
d_24METMETMETMETBB114 - 158114 - 158
d_25GLNGLNGLYGLYBB160 - 259160 - 259
d_31METMETLEULEUCC1 - 551 - 55
d_32LYSLYSGLYGLYCC57 - 7557 - 75
d_33PHEPHELEULEUCC77 - 11277 - 112
d_34METMETMETMETCC114 - 158114 - 158
d_35GLNGLNGLYGLYCC160 - 259160 - 259
d_41METMETLEULEUDD1 - 551 - 55
d_42LYSLYSGLYGLYDD57 - 7557 - 75
d_43PHEPHELEULEUDD77 - 11277 - 112
d_44METMETMETMETDD114 - 158114 - 158
d_45GLNGLNGLYGLYDD160 - 259160 - 259
d_51METMETLEULEUEE1 - 551 - 55
d_52LYSLYSGLYGLYEE57 - 7557 - 75
d_53PHEPHELEULEUEE77 - 11277 - 112
d_54METMETMETMETEE114 - 158114 - 158
d_55GLNGLNGLYGLYEE160 - 259160 - 259
d_61METMETLEULEUFF1 - 551 - 55
d_62LYSLYSGLYGLYFF57 - 7557 - 75
d_63PHEPHELEULEUFF77 - 11277 - 112
d_64METMETMETMETFF114 - 158114 - 158
d_65GLNGLNGLYGLYFF160 - 259160 - 259

NCS oper:
IDCodeMatrixVector
1given(-0.429384958131, 0.763297899142, -0.482705785024), (0.762649205802, 0.0201782428193, -0.646497507656), (-0.483730034854, -0.645731488842, -0.590792770519)-39.1883278581, 98.0318869351, 108.185823085
2given(0.980471014659, 0.196111615679, -0.0147249315818), (-0.196080638534, 0.980581410016, 0.003532919928), (0.015131840808, -0.000576651599584, 0.99988534086)-76.5574494194, 37.7517443942, -5.89289409227
3given(-0.264815249345, 0.757264305708, -0.597012273756), (0.831294102122, -0.134484357537, -0.539318155967), (-0.488695201012, -0.639112454016, -0.593895842408)-96.8075747333, 142.008227373, 101.920528755
4given(0.56941726766, -0.820542468246, 0.0497396531526), (-0.821686800144, -0.56991886908, 0.00482546742212), (0.0243880659241, -0.0436181209139, -0.998750560334)57.4621984723, 185.155107178, 99.2779862967
5given(-0.893163216866, 0.388028716325, 0.227361349714), (-0.0798885751891, -0.634397326614, 0.768867899928), (0.442580256667, 0.668560952563, 0.59761941829)-40.1251219257, 161.018008582, -14.3766742795

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Prolyl oligopeptidase family protein


Mass: 29203.551 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria)
Gene: ThesiDRAFT1_1468 / Production host: Escherichia coli (E. coli) / References: UniProt: I9KU82

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Non-polymers , 5 types, 352 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.61 Å3/Da / Density % sol: 52.84 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 5% PEG 6000 0.1 M Tris-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9763 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.42→20 Å / Num. obs: 67696 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 46.54 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.75
Reflection shellResolution: 2.42→2.46 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 3350

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q4H

7q4h


Resolution: 2.42→19.94 Å / SU ML: 0.3685 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 2051 3.03 %
Rwork0.217 65618 -
obs0.2182 67669 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.07 Å2
Refinement stepCycle: LAST / Resolution: 2.42→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12246 0 66 340 12652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006712538
X-RAY DIFFRACTIONf_angle_d1.025816823
X-RAY DIFFRACTIONf_chiral_restr0.06021831
X-RAY DIFFRACTIONf_plane_restr0.00922150
X-RAY DIFFRACTIONf_dihedral_angle_d5.25111657
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.798289213624
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.490721726899
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.879724916667
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.53630019155
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.908945131091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.480.31471280.27494371X-RAY DIFFRACTION99.03
2.48-2.540.29141100.2594366X-RAY DIFFRACTION99.91
2.54-2.610.2831570.25554401X-RAY DIFFRACTION99.96
2.61-2.680.39781250.25274357X-RAY DIFFRACTION100
2.68-2.770.30861450.25234370X-RAY DIFFRACTION99.93
2.77-2.870.31761490.25944347X-RAY DIFFRACTION99.96
2.87-2.980.30421120.25434438X-RAY DIFFRACTION99.96
2.98-3.120.32461340.24354356X-RAY DIFFRACTION99.93
3.12-3.280.29051330.23364401X-RAY DIFFRACTION100
3.28-3.490.25791380.22354361X-RAY DIFFRACTION100
3.49-3.750.26071360.20794388X-RAY DIFFRACTION100
3.75-4.130.26241280.20064386X-RAY DIFFRACTION100
4.13-4.720.20011400.18654358X-RAY DIFFRACTION99.93
4.72-5.920.20721520.1924362X-RAY DIFFRACTION99.93
5.92-19.940.22291640.20484356X-RAY DIFFRACTION99.91
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)
12.771098148320.102407299153-0.06030421299282.300487523630.2559616897562.081201225850.05547522036490.08498904366430.2193208373510.2591829580280.1720153863770.476519520788-0.322848584084-0.251101723305-0.2146110513350.3465972918290.04417837554320.1009157762130.245176324010.08431937481470.355870345023-0.639176203053100.60513397331.1324382015
21.298566998970.272328000365-0.4475922473662.6885209267-0.4872517198741.986128018210.07646490229140.154880681236-0.26927489414-0.06677912984640.00142353584584-0.3732597471780.05868692756340.269730084893-0.06403820534210.2113353357880.0196106966574-0.005567075714710.322450200285-0.06386127823860.31955723300722.795215623279.322211957825.1368544633
32.02590644983-0.6715053170090.5131333080823.843857705241.295137528953.29348203255-0.04122375483880.2508346286580.267632434479-0.48130574635-0.173027584756-0.275079123223-0.468277607640.0258538610220.2125649289360.393678558148-0.0839343532636-0.04598608742440.4495757301310.03999546566250.375341223533-57.9776871983136.60965115425.2335344722
42.67684587096-0.9319758218120.1846726266652.905639199011.018268550512.07432948120.08408382859740.837106106317-0.260946198871-0.1323805145770.179589135392-0.9215103129490.3001061172530.790648460432-0.2468899086110.4547833219870.07630571299740.06918152382670.855922844044-0.1458778958180.77141275568-39.1380932284111.03638336419.4274723953
52.081109320450.4092299157530.5578129698542.43200707908-0.6244721287761.96042618707-0.0921410570657-0.141944144201-0.154631003071-0.232837793767-0.08153627890390.1085633445550.454010614653-0.647647339970.1713907829350.47515182015-0.1234289414580.1016335127030.590334449808-0.1774933537760.459949545822-23.8987762522128.55825894263.7180051529
62.23925778180.5651869304970.6446362826221.28225427291-0.4462019369381.852500427110.0313052751173-0.114099424436-0.3004303241460.281901872355-0.146565045582-0.4555510511520.4025009814420.2220645302630.1219289605740.6867478762590.1695779866270.02720156969860.5030549104660.0531583761920.5831669821386.65005269649121.29674089471.2082368009
72.913224531240.75587802713-0.4000691438554.28597540155-0.6729365732021.040242175840.29893695881-0.5353237904080.1728834956670.566414713212-0.2242112847730.00349454903395-0.607653423515-0.0704831583566-0.08243538904550.6758120318180.00192110698090.1119391709560.4082918234590.0184764007220.3389698603525.6796253966689.688574867852.0040600791
85.52438071269-0.6977986724280.9689956029270.799787870479-0.1250846545250.1689379506420.3070615240150.261507658825-0.973982216587-0.1534914920990.00605311965123-0.1580520116730.410599186479-0.19991459827-0.3781770533380.51803969616-0.0889478425171-0.05740848922120.462153204413-0.05612795599670.4454734421421.7514114402870.893888239916.7733996962
92.73581454028-0.6221466495270.2679892143384.706840381810.1762602780240.642492368455-0.224259508873-0.5909731837630.2195994226780.7967387443790.0335443535652-0.649049857470.342430407126-0.2573906402020.1524377056440.6599754671590.0196498297516-0.1387214193990.4688270187580.01595274660070.436959322209-54.0389840623124.76209919646.1056892658
103.44309618187-0.1436627818852.093994892481.99864318135-0.8246351855381.549838119560.2268910546860.441530694732-0.492736781532-0.0787864230362-0.2874270047260.1168177842390.1380143733570.296391295446-0.01035157263940.5423335492220.0701795743330.002869454199280.766346886636-0.115319471780.507545895014-61.3555608361106.85025402510.8892861636
116.884838636861.6567505050.3585989557351.70681938536-0.6408193070212.08351775638-0.4218022967040.201076437486-0.477835836841-0.186737005954-0.1288605745080.5028242619890.449532655802-0.5001880700120.6039465998480.497394192067-0.03666222254810.111929081840.432946002791-0.1631113692330.493366844747-10.2844978588129.67775306543.4286559319
126.52034127186-2.997666580891.610535405393.564292594950.2259218318761.50066586328-0.580493086542-0.4727845112280.4104083026210.51232556750.332692057792-0.6275902239220.4097502642860.5287642875650.197253282660.6077349270540.0969004858339-0.07293617324520.4817398371590.01159302391480.418067266821.01961002506143.6340408579.3223501354
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and ((resid 1:140) or (resid 183:259)))AA1 - 2591 - 259
22(chain 'B' and ((resid 1:140) or (resid 183:259)))BD1 - 2591 - 259
33(chain 'C' and ((resid 1:140) or (resid 183:259)))CF1 - 2591 - 259
44(chain 'D' and ((resid 1:140) or (resid 183:259)))DH1 - 2591 - 259
55(chain 'E' and ((resid 1:140) or (resid 183:259)))EI1 - 2591 - 259
66(chain 'F' and ((resid 1:140) or (resid 183:259)))FK1 - 2591 - 259
77(chain 'A' and (resid 141:182))AA141 - 182141 - 182
88(chain 'B' and (resid 141:182))BD141 - 182141 - 182
99(chain 'C' and (resid 141:182))CF141 - 182141 - 182
1010(chain 'D' and (resid 141:182))DH141 - 182141 - 182
1111(chain 'E' and (resid 141:182))EI141 - 182141 - 182
1212(chain 'F' and (resid 141:182))FK141 - 182141 - 182

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