[English] 日本語
Yorodumi
- PDB-6xs3: X-ray structure of the monoclinic crystal form at 2.48 A resoluti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xs3
TitleX-ray structure of the monoclinic crystal form at 2.48 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 298 K
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / substrate complex / diacylglycerol / covalent intermediate / interfacial activation
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride 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 / OCTANOIC ACID (CAPRYLIC ACID) / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 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 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
B: Lipase
C: Lipase
E: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,34637
Polymers191,0196
Non-polymers7,32731
Water7,710428
1
A: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,08517
Polymers95,5093
Non-polymers3,57614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-57 kcal/mol
Surface area29450 Å2
MethodPISA
2
B: Lipase
C: Lipase
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,26120
Polymers95,5093
Non-polymers3,75117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-69 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.185, 91.366, 124.316
Angle α, β, γ (deg.)90.000, 94.700, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 12 molecules ABCEDF

#1: Protein
Lipase / / Triacylglycerol lipase


Mass: 31836.459 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Gene: LIP / Production host: Aspergillus aculeatinus (mold) / References: UniProt: O59952, triacylglycerol lipase
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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 , 5 types, 453 molecules

#2: Chemical
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H16O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-LTV / 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate


Mass: 723.204 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C46H90O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.32 Å3/Da / Density % sol: 46.91 % / Description: cube shaped blocks
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: CXrystals were grown by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1M MES buffer. The drops were 6 ul composed of equal amounts of protein at 30 mg/ml in ...Details: CXrystals were grown by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1M MES buffer. The drops were 6 ul composed of equal amounts of protein at 30 mg/ml in water with the reservoir solution. Temperature was 298 K and crystals appeared after about two weeks
PH range: 6.0 - 7.0

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Jun 20, 2017
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.48→75 Å / Num. obs: 81074 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 26 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.102 / Rrim(I) all: 0.327 / Rsym value: 0.287 / Net I/σ(I): 7.1
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4362 / CC1/2: 0.18 / Rpim(I) all: 0.62 / Rrim(I) all: 1.3 / Rsym value: 1.01 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 2.48→51.27 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.19 / Stereochemistry target values: ML
Details: Structure was refined to convergence with REFMAC5 in CCP4, then five runs through PHENIX REFINE using isotropic B values and no TLS.
RfactorNum. reflection% reflection
Rfree0.2134 3025 4.91 %
Rwork0.1783 58636 -
obs0.1801 61661 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164 Å2 / Biso mean: 36.1154 Å2 / Biso min: 9.62 Å2
Refinement stepCycle: final / Resolution: 2.48→51.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12425 0 508 430 13363
Biso mean--72.84 32.57 -
Num. residues----1614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-2.520.3481310.3142533266494
2.52-2.560.27621500.29582564271498
2.56-2.60.3291210.27912683280499
2.6-2.650.30721350.26882627276299
2.65-2.70.28831470.25942659280699
2.7-2.760.28871420.246726482790100
2.76-2.820.2611470.235326472794100
2.82-2.880.24451370.226326522789100
2.88-2.960.26061430.208626722815100
2.96-3.040.24111530.204426502803100
3.04-3.130.23041340.19426772811100
3.13-3.230.23231410.188526532794100
3.23-3.340.23651370.177626752812100
3.34-3.480.21861440.175426582802100
3.48-3.630.1731240.153327042828100
3.63-3.820.17221250.142526852810100
3.83-4.060.19611280.13926852813100
4.06-4.380.15981330.129626822815100
4.38-4.820.16851450.11527112856100
4.82-5.510.15291260.129327032829100
5.51-6.940.17561310.151227172848100
6.95-51.270.16711510.157627512902100

+
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