[English] 日本語
Yorodumi
- PDB-7q4j: A thermostable lipase from Thermoanaerobacter thermohydrosulfuric... -

+
Open data


ID or keywords:

Loading...

-
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 / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DECANE / nonane / N-OCTANE / STEARIC ACID / Serine aminopeptidase S33 domain-containing protein
Similarity search - Component
Biological speciesThermoanaerobacter thermohydrosulfuricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 8 types, 305 molecules

#3: Chemical ChemComp-STE / 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


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


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.75 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

-
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

-
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

+
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