[English] 日本語
Yorodumi
- PDB-7kaz: Crystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kaz
TitleCrystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staphylococcus aureus
ComponentsOleate hydratase
KeywordsOXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / 18:1 / complex / oleic acid / hydroxystearic acid / FAD / h18:0
Function / homology
Function and homology information


oleate hydratase / oleate hydratase activity / FAD binding / fatty acid metabolic process
Similarity search - Function
Oleate hydratase / MCRA family / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / OLEIC ACID / (10R)-10-hydroxyoctadecanoic acid / Myosin-cross-reactive antigen
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsRadka, C.D. / Rock, C.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA21765 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structure and mechanism of Staphylococcus aureus oleate hydratase (OhyA).
Authors: Radka, C.D. / Batte, J.L. / Frank, M.W. / Young, B.M. / Rock, C.O.
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 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
C: Oleate hydratase
B: Oleate hydratase
A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,9809
Polymers209,5043
Non-polymers2,4766
Water49,0912725
1
C: Oleate hydratase
A: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0776
Polymers139,6692
Non-polymers1,4084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-21 kcal/mol
Surface area42040 Å2
MethodPISA
2
B: Oleate hydratase
hetero molecules

B: Oleate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8056
Polymers139,6692
Non-polymers2,1364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9430 Å2
ΔGint-22 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.022, 113.085, 118.393
Angle α, β, γ (deg.)90.000, 116.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1613-

HOH

21B-943-

HOH

31B-1362-

HOH

41B-1604-

HOH

-
Components

-
Protein , 1 types, 3 molecules CBA

#1: Protein Oleate hydratase / / Myosin-cross-reactive antigen


Mass: 69834.688 Da / Num. of mol.: 3 / Mutation: E82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_ ...Gene: DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_02399, NCTC10654_00136, RK64_00980
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6GJV1

-
Non-polymers , 5 types, 2731 molecules

#2: Chemical ChemComp-WAD / (10R)-10-hydroxyoctadecanoic acid / (R)-10-Hydroxystearic acid


Mass: 300.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2725 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and ...Details: Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and 750 uM FAD. Cryo: 15% v/v PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, 30% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→22.42 Å / Num. obs: 183821 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.04 / Net I/σ(I): 6.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.8 % / Num. unique obs: 18078 / Rpim(I) all: 0.485 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
KYLINdata reduction
KYLINdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KAV

7kav


Resolution: 1.854→22.42 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 2005 1.09 %
Rwork0.1936 181771 -
obs0.1942 183776 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.29 Å2 / Biso mean: 29.2785 Å2 / Biso min: 6.04 Å2
Refinement stepCycle: final / Resolution: 1.854→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14099 0 331 2725 17155
Biso mean--35.06 37.68 -
Num. residues----1746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414613
X-RAY DIFFRACTIONf_angle_d1.16219802
X-RAY DIFFRACTIONf_dihedral_angle_d6.978710
X-RAY DIFFRACTIONf_chiral_restr0.0632162
X-RAY DIFFRACTIONf_plane_restr0.0082515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.854-1.90020.4311410.37021266596
1.9002-1.95150.39831480.34081302599
1.9515-2.00890.3821350.30981297599
2.0089-2.07370.3181360.28041272597
2.0737-2.14780.29581490.23641303099
2.1478-2.23370.25331470.20241303099
2.2337-2.33530.24491370.18321308099
2.3353-2.45830.23861500.17671307499
2.4583-2.61210.24071460.1811309799
2.6121-2.81340.26881430.17751303199
2.8134-3.09580.23221390.1711277297
3.0958-3.54230.19711490.14491315499
3.5423-4.45720.17651380.13441305199
4.4572-22.420.23271470.18711306297

+
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