[English] 日本語
Yorodumi
- PDB-6alw: The crystal structure of the Staphylococcus aureus Fatty acid Kin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6alw
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with 12-Methyl Myristic Acid (C15:0) to 1.63 Angstrom resolution
ComponentsEDD domain protein, DegV family
KeywordsTRANSFERASE / Staphylococcus aureus / FakB1 / 12-Methyl Myristic Acid / 12-Methyltetradecanoic acid / C15:0
Function / homology
Function and homology information


Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / : / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(12R)-12-methyltetradecanoic acid / (12S)-12-methyltetradecanoic acid / DegV domain-containing protein / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsCuypers, M.G. / Ericson, M. / Subramanian, C. / White, S.W. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
St. Jude Children's Research Hospital (ALSAC) United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Acyl-chain selectivity and physiological roles ofStaphylococcus aureusfatty acid-binding proteins.
Authors: Cuypers, M.G. / Subramanian, C. / Gullett, J.M. / Frank, M.W. / White, S.W. / Rock, C.O.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: EDD domain protein, DegV family
B: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90914
Polymers64,2032
Non-polymers1,70612
Water15,097838
1
A: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1399
Polymers32,1021
Non-polymers1,0378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7705
Polymers32,1021
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.348, 54.529, 84.415
Angle α, β, γ (deg.)105.13, 90.00, 107.81
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein EDD domain protein, DegV family / EDD / DegV family domain protein / Fatty acid-binding protein DegV / FakB1 protein


Mass: 32101.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: AYM28_04055, AYM37_04055, ERS072738_00223, ERS072840_01626, ERS074020_00218, HMPREF3211_01094
Production host: Escherichia coli (E. coli) / References: UniProt: X5EH37, UniProt: P0A0N2*PLUS
#2: Chemical ChemComp-BNV / (12S)-12-methyltetradecanoic acid


Mass: 242.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O2
#3: Chemical ChemComp-BMJ / (12R)-12-methyltetradecanoic acid


Mass: 242.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PH 6.5 0.1M MES/IMIDAZOLE, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03M NaNO3, 0.03M NA2HPO4, 0.03M (NH4)2 SO4
Temp details: controlled room temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: crystal flash frozen in Liq. N2
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→81.18 Å / Num. obs: 66112 / % possible obs: 97.2 % / Redundancy: 4 % / Biso Wilson estimate: 7.76 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.106 / Rrim(I) all: 0.212 / Net I/σ(I): 8.6
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2 / Num. unique obs: 3294 / CC1/2: 0.662 / Rpim(I) all: 0.524 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTO

5uto


Resolution: 1.63→40.591 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3305 5 %random
Rwork0.1549 ---
obs0.1571 66100 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→40.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 116 838 5407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014856
X-RAY DIFFRACTIONf_angle_d0.9526561
X-RAY DIFFRACTIONf_dihedral_angle_d13.6342960
X-RAY DIFFRACTIONf_chiral_restr0.067727
X-RAY DIFFRACTIONf_plane_restr0.006849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.65330.27431400.2512613X-RAY DIFFRACTION95
1.6533-1.6780.27831340.23452556X-RAY DIFFRACTION96
1.678-1.70420.2371330.22792575X-RAY DIFFRACTION96
1.7042-1.73210.26611220.21192563X-RAY DIFFRACTION96
1.7321-1.7620.261520.20942615X-RAY DIFFRACTION96
1.762-1.7940.24631160.19382589X-RAY DIFFRACTION96
1.794-1.82850.23211070.182594X-RAY DIFFRACTION96
1.8285-1.86590.21591440.17232615X-RAY DIFFRACTION96
1.8659-1.90640.17541400.16812569X-RAY DIFFRACTION97
1.9064-1.95080.22791310.17442637X-RAY DIFFRACTION96
1.9508-1.99960.2341120.17252596X-RAY DIFFRACTION97
1.9996-2.05360.24321510.16892568X-RAY DIFFRACTION97
2.0536-2.11410.16371700.14972634X-RAY DIFFRACTION97
2.1141-2.18230.19981550.14922620X-RAY DIFFRACTION97
2.1823-2.26030.2141240.14832613X-RAY DIFFRACTION97
2.2603-2.35080.18021480.14912591X-RAY DIFFRACTION98
2.3508-2.45770.21331570.15122599X-RAY DIFFRACTION98
2.4577-2.58730.19221370.15612720X-RAY DIFFRACTION98
2.5873-2.74940.17481110.14672638X-RAY DIFFRACTION98
2.7494-2.96160.20531300.14432612X-RAY DIFFRACTION98
2.9616-3.25950.18971460.13892691X-RAY DIFFRACTION99
3.2595-3.73090.17411630.12082644X-RAY DIFFRACTION99
3.7309-4.69940.14361400.10922662X-RAY DIFFRACTION99
4.6994-40.60330.1621420.14082681X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.2649 Å / Origin y: -0.9655 Å / Origin z: -0.289 Å
111213212223313233
T0.0331 Å2-0.004 Å2-0.0006 Å2-0.0479 Å20.0023 Å2--0.0556 Å2
L0.0831 °2-0.0291 °2-0.0454 °2-0.2573 °20.3004 °2--0.78 °2
S-0.0142 Å °-0.006 Å °0.0033 Å °0.0118 Å °-0.0101 Å °0.0109 Å °0.0067 Å °0.0172 Å °0.0118 Å °
Refinement TLS groupSelection details: all

+
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