[English] 日本語
Yorodumi
- PDB-6kf5: Microbial Hormone-sensitive lipase E53 mutant I256L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kf5
TitleMicrobial Hormone-sensitive lipase E53 mutant I256L
ComponentsLipase
KeywordsHYDROLASE / Esterase / Microbial Hormone-sensitive lipase
Function / homology
Function and homology information


: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SUPEROXO ION / HEXANOIC ACID / (4-nitrophenyl) hexanoate / Lipase
Similarity search - Component
Biological speciesErythrobacter longus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYang, X. / Li, Z.Y. / Li, J. / Xu, X.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31770004 China
CitationJournal: To Be Published
Title: Microbial Hormone-sensitive lipase E53 mutant I256L
Authors: Yang, X. / Yingyi, H. / Li, Z.Y. / Shuling, J. / Zhen, R. / Zhao, W. / Xiaojian, H. / Henglin, C. / Li, J. / Xu, X.W.
History
DepositionJul 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,65521
Polymers132,6354
Non-polymers2,02017
Water18,7721042
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.772, 129.603, 219.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11B-718-

HOH

21B-730-

HOH

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Lipase


Mass: 33158.730 Da / Num. of mol.: 4 / Mutation: I256L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter longus (bacteria) / Gene: EH31_02760
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A074MDU6

-
Non-polymers , 6 types, 1059 molecules

#2: Chemical
ChemComp-D8F / (4-nitrophenyl) hexanoate


Mass: 237.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2FK / SUPEROXO ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Calcium chloride, Bis-Tris, PEG MME 550, pH 6.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.09→19.5 Å / Num. obs: 119275 / % possible obs: 99.4 % / Redundancy: 13.1 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.178 / Net I/σ(I): 17.4
Reflection shellResolution: 2.09→2.13 Å / Num. unique obs: 11668 / CC1/2: 0.893

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 2.09→19.5 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3992
RfactorNum. reflection% reflection
Rfree0.214 5874 4.93 %
Rwork0.1829 --
obs0.1844 119096 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.79 Å2
Refinement stepCycle: LAST / Resolution: 2.09→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9111 0 138 1042 10291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00739438
X-RAY DIFFRACTIONf_angle_d0.877512853
X-RAY DIFFRACTIONf_chiral_restr0.05261475
X-RAY DIFFRACTIONf_plane_restr0.00611701
X-RAY DIFFRACTIONf_dihedral_angle_d5.62375681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.27922050.23253601X-RAY DIFFRACTION97.02
2.12-2.140.26562020.22823751X-RAY DIFFRACTION99.6
2.14-2.170.23541970.21663708X-RAY DIFFRACTION99.87
2.17-2.20.24931810.20623740X-RAY DIFFRACTION99.82
2.2-2.220.24471940.20383742X-RAY DIFFRACTION99.72
2.22-2.250.2622190.20123702X-RAY DIFFRACTION99.67
2.25-2.290.2562000.19713754X-RAY DIFFRACTION99.75
2.29-2.320.24462100.18933704X-RAY DIFFRACTION99.8
2.32-2.360.22911860.19113805X-RAY DIFFRACTION99.73
2.36-2.40.2051950.18423701X-RAY DIFFRACTION99.87
2.4-2.440.23162140.19123770X-RAY DIFFRACTION99.95
2.44-2.480.21641970.18773720X-RAY DIFFRACTION99.9
2.48-2.530.25211840.18693794X-RAY DIFFRACTION99.95
2.53-2.580.21851640.18123776X-RAY DIFFRACTION99.95
2.58-2.640.20881980.18063790X-RAY DIFFRACTION99.92
2.64-2.70.21922240.1813713X-RAY DIFFRACTION99.95
2.7-2.760.1941890.17763781X-RAY DIFFRACTION99.95
2.76-2.840.20921940.17643804X-RAY DIFFRACTION100
2.84-2.920.23671990.18413764X-RAY DIFFRACTION99.97
2.92-3.020.19611890.17643800X-RAY DIFFRACTION99.95
3.02-3.120.22781710.18523791X-RAY DIFFRACTION100
3.12-3.250.22831770.18093831X-RAY DIFFRACTION99.98
3.25-3.40.18152090.18143803X-RAY DIFFRACTION99.9
3.4-3.570.2162030.17153772X-RAY DIFFRACTION99.8
3.57-3.80.20022100.17473798X-RAY DIFFRACTION99.68
3.8-4.090.20571970.15923824X-RAY DIFFRACTION99.55
4.09-4.490.17421920.15393845X-RAY DIFFRACTION99.75
4.49-5.130.17981920.16113854X-RAY DIFFRACTION99.58
5.13-6.430.23441790.20383927X-RAY DIFFRACTION99.44
6.43-19.50.2152030.21283857X-RAY DIFFRACTION95.17

+
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