[English] 日本語
Yorodumi
- PDB-6ksl: Staphylococcus aureus lipase - S116A inactive mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ksl
TitleStaphylococcus aureus lipase - S116A inactive mutant
ComponentsLipase 2
KeywordsHYDROLASE / fatty acid binding
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Lipase-like, C-terminal domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
butanoic acid / LAURIC ACID / triacylglycerol lipase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsKitadokoro, K. / Tanaka, M. / Kamitani, S.
Citation
Journal: Sci Rep / Year: 2020
Title: Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat.
Authors: Kitadokoro, K. / Tanaka, M. / Hikima, T. / Okuno, Y. / Yamamoto, M. / Kamitani, S.
#1: Journal: Sci Rep / Year: 2020
Title: Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat.
Authors: Kitadokoro, K. / Tanaka, M. / Hikima, T. / Okuno, Y. / Yamamoto, M. / Kamitani, S.
#2: Journal: To Be Published
Title: Anti-Obesity drug of Human gastric lipase inhibits pathogenic Staphylococcus aureus lipase.
Authors: Kitadokoro, K. / Tanaka, M. / Kamitani, S.
History
DepositionAug 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase 2
B: Lipase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55111
Polymers91,5632
Non-polymers9889
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.209, 164.209, 233.053
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Lipase 2


Mass: 45781.391 Da / Num. of mol.: 2 / Mutation: S116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lip, BN1321_80040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1MWF9, triacylglycerol lipase

-
Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Sequence detailsE68Q was genetic variant.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.3 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.0M Ammonium phosphate dibasic, 0.1M Tris pH8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 109044 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 65 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.083 / Net I/σ(I): 16.8
Reflection shellResolution: 2.59→2.75 Å / Num. unique obs: 17409 / CC1/2: 0.523 / Rrim(I) all: 2.138

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KSI

6ksi


Resolution: 2.59→48.81 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 2901 5 %RANDOM
Rwork0.2493 55105 --
obs0.2503 58006 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.39 Å2 / Biso mean: 65.5405 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.59→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 58 12 6116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196259
X-RAY DIFFRACTIONr_bond_other_d00.025603
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9368471
X-RAY DIFFRACTIONr_angle_other_deg3.93313022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79924.183306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.64915994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9511530
X-RAY DIFFRACTIONr_chiral_restr0.1750.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217052
X-RAY DIFFRACTIONr_gen_planes_other0.010.021326
X-RAY DIFFRACTIONr_mcbond_it4.3146.3933054
X-RAY DIFFRACTIONr_mcbond_other4.3126.3923053
X-RAY DIFFRACTIONr_mcangle_it6.29.5853814
LS refinement shellResolution: 2.591→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 206 -
Rwork0.409 3902 -
all-4108 -
obs--97.69 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-58.00251.691-1.969
2-64.44563.904-7.812
3-61.98434.1395.925
4-25.54283.759-11.925
5-24.19788.3282.31
6-15.81674.959-26.64
7-47.34371.284-4.324
8-29.12266.105-8.884
9-45.52162.935-8.569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 385
2X-RAY DIFFRACTION2A401
3X-RAY DIFFRACTION3A402
4X-RAY DIFFRACTION4B4 - 385
5X-RAY DIFFRACTION5B401
6X-RAY DIFFRACTION6B402
7X-RAY DIFFRACTION7A501 - 507
8X-RAY DIFFRACTION7B501 - 505
9X-RAY DIFFRACTION8A403
10X-RAY DIFFRACTION8B403 - 404
11X-RAY DIFFRACTION9A404
12X-RAY DIFFRACTION9B405

+
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