[English] 日本語
Yorodumi
- PDB-8b9s: NATIVE FORM, THERMOSTABLE LIPASE FROM THERMOANAEROBACTER THERMOHY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b9s
TitleNATIVE FORM, THERMOSTABLE LIPASE FROM THERMOANAEROBACTER THERMOHYDROSULFURICUS
ComponentsProlyl oligopeptidase family protein
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / THERMOSTABLE
Function / homology: / Serine 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 352 molecules

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


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


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


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more