[English] 日本語
Yorodumi
- PDB-6xok: X-ray structure of the rhombohedral form of the lipase from Therm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xok
TitleX-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / diacylglyceride / interfacial activation / oligomer / substrate complex
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / : / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-LTV / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMcPherson, A.
CitationJournal: Current Enzyme Inhibition / Year: 2020
Title: The crystal Structures of Thermomyces (Humicola) lanuginosa lipase in complex with enzymatic reactants
Authors: McPherson, A. / Larson, S.B. / Kalasky, A.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54510
Polymers31,8361
Non-polymers1,7089
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)201,27060
Polymers191,0196
Non-polymers10,25154
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area22650 Å2
ΔGint-214 kcal/mol
Surface area56500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.373, 76.373, 241.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-244-

THR

21A-307-

PO4

31A-307-

PO4

41A-686-

HOH

51A-801-

HOH

61A-816-

HOH

71A-819-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lipase / Triacylglycerol lipase


Mass: 31836.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Gene: LIP / Production host: Aspergillus flavus (mold) / References: UniProt: O59952, triacylglycerol lipase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 435 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-LTV / 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate


Mass: 723.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H90O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.23 % / Description: thin needles of indeterminate cross section
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals were grown by vapor diffusion at room temperature in 24 well Cryschem sitting drop plates (Hampton Research, Aliso Viejo, CA) with 600 microleters reservoirs of 25% PEG 3350 in 0.10 ...Details: Crystals were grown by vapor diffusion at room temperature in 24 well Cryschem sitting drop plates (Hampton Research, Aliso Viejo, CA) with 600 microleters reservoirs of 25% PEG 3350 in 0.10 M MES buffer at pH 6.5. The protein droplets were of 8ul volume and consisted of equal parts of a 20 to 30 mg/ml protein stock solution and the reservoir solution. Crystals usually appeared and grew to full size within one to two weeks. Rhombohedral crystals were thin needles of indeterminate cross-section
PH range: 6.0 - 7.0

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Feb 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.3→80 Å / Num. obs: 58358 / % possible obs: 88 % / Redundancy: 31 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.008 / Rrim(I) all: 0.05 / Rsym value: 0.049 / Net I/σ(I): 42.7
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 463 / CC1/2: 0.81 / Rpim(I) all: 0.205 / Rrim(I) all: 0.461 / Rsym value: 0.36 / % possible all: 14.4

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 1.3→80 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.3452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Structure was thoroughly refined using REFMAC5 from CCP4 but then refined further using REFINE from PHENIX. Some improvements, such as addition of aa 241-244 at the cleavage site were made ...Details: Structure was thoroughly refined using REFMAC5 from CCP4 but then refined further using REFINE from PHENIX. Some improvements, such as addition of aa 241-244 at the cleavage site were made in REFINE. The restraints for the diglyceride substrate were made in the GRADE server. Waters were added by hand.
RfactorNum. reflection% reflection
Rfree0.1343 2865 4.91 %
Rwork0.1041 55488 -
obs0.1056 58353 87.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.44 Å2
Refinement stepCycle: LAST / Resolution: 1.3→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 108 427 2550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792340
X-RAY DIFFRACTIONf_angle_d1.24433189
X-RAY DIFFRACTIONf_chiral_restr0.0991342
X-RAY DIFFRACTIONf_plane_restr0.0072410
X-RAY DIFFRACTIONf_dihedral_angle_d20.1882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.1926140.1575459X-RAY DIFFRACTION14.42
1.33-1.350.1646680.11691178X-RAY DIFFRACTION37.91
1.35-1.380.1411150.10061748X-RAY DIFFRACTION57.01
1.38-1.410.15341030.08672327X-RAY DIFFRACTION74.11
1.41-1.440.13711300.082686X-RAY DIFFRACTION85.57
1.44-1.470.11931930.07562831X-RAY DIFFRACTION92.31
1.47-1.510.11581590.07153015X-RAY DIFFRACTION96.07
1.51-1.550.12521430.07613079X-RAY DIFFRACTION98.53
1.55-1.590.1141320.07563189X-RAY DIFFRACTION99.91
1.59-1.640.12121650.07993095X-RAY DIFFRACTION100
1.64-1.70.12971390.08113181X-RAY DIFFRACTION100
1.7-1.770.11821570.08853142X-RAY DIFFRACTION100
1.77-1.850.12991760.08633119X-RAY DIFFRACTION99.97
1.85-1.950.12911500.08813178X-RAY DIFFRACTION100
1.95-2.070.11481480.08743176X-RAY DIFFRACTION100
2.07-2.230.12951920.08783131X-RAY DIFFRACTION100
2.23-2.460.11741540.09483196X-RAY DIFFRACTION100
2.46-2.810.12851540.11273201X-RAY DIFFRACTION100
2.81-3.540.14171780.11363222X-RAY DIFFRACTION100
3.54-80.520.15561950.14173335X-RAY DIFFRACTION99.92

+
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