[English] 日本語
Yorodumi
- PDB-6ksm: Staphylococcus aureus lipase -Orlistat complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ksm
TitleStaphylococcus aureus lipase -Orlistat complex
ComponentsLipase 2
KeywordsHYDROLASE / Orlistat binding
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process
Similarity search - Function
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 / Chem-DH9 / STEARIC ACID / triacylglycerol lipase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKitadokoro, K. / Tanaka, M. / Kamitani, S.
CitationJournal: 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.
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 / struct_conn / struct_conn_type
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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

-
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)94,09515
Polymers91,5952
Non-polymers2,50013
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-37 kcal/mol
Surface area33000 Å2
Unit cell
Length a, b, c (Å)132.510, 132.510, 248.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Lipase 2 /


Mass: 45797.391 Da / Num. of mol.: 2
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 , 7 types, 73 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-DH9 / (2S,3S,5S)-5-[(N-FORMYL-L-LEUCYL)OXY]-2-HEXYL-3-HYDROXYHEXADECANOIC ACID


Mass: 513.750 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H55NO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BUA / butanoic acid / Butyric acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 6.4 Å3/Da / Density % sol: 80.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.0M Sodium Formate, 0.1M Sodium Acetate pH4.5

-
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: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 205262 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 45.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.125 / Net I/σ(I): 10.6
Reflection shellResolution: 2.23→2.37 Å / Num. unique obs: 32762 / CC1/2: 0.424 / Rrim(I) all: 2.573

-
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: 2.23→48.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 5386 5 %RANDOM
Rwork0.2259 102334 --
obs0.2275 107720 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.5 Å2 / Biso mean: 47.0476 Å2 / Biso min: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.23→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6040 0 164 60 6264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0196355
X-RAY DIFFRACTIONr_bond_other_d00.025761
X-RAY DIFFRACTIONr_angle_refined_deg2.6031.958577
X-RAY DIFFRACTIONr_angle_other_deg3.928313402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7495762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10724.145304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69715992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9511530
X-RAY DIFFRACTIONr_chiral_restr0.2370.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217080
X-RAY DIFFRACTIONr_gen_planes_other0.0230.021334
X-RAY DIFFRACTIONr_mcbond_it3.2994.4343054
X-RAY DIFFRACTIONr_mcbond_other3.294.4333053
X-RAY DIFFRACTIONr_mcangle_it4.7876.633814
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 382 -
Rwork0.42 7260 -
all-7642 -
obs--97.02 %
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)
116.86426.654-11.562
264.33536.394-24.218
336.95934.885-28.32
443.9328.553-7.859
541.00832.606-16.54
637.18331.67-27.497
744.2837.805-28.421
832.37532.449-17.303
939.79232.46-19.925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 385
2X-RAY DIFFRACTION2B4 - 385
3X-RAY DIFFRACTION3A401
4X-RAY DIFFRACTION3B401
5X-RAY DIFFRACTION4A402
6X-RAY DIFFRACTION4B402
7X-RAY DIFFRACTION5A403
8X-RAY DIFFRACTION5B403
9X-RAY DIFFRACTION6A404 - 405
10X-RAY DIFFRACTION6B404 - 405
11X-RAY DIFFRACTION7B406
12X-RAY DIFFRACTION8A501 - 534
13X-RAY DIFFRACTION8B501 - 526
14X-RAY DIFFRACTION9A406
15X-RAY DIFFRACTION9B407

+
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