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- PDB-7ed6: Crystal structure of Thermus thermophilus FakA ATP-binding domain -

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Basic information

Entry
Database: PDB / ID: 7ed6
TitleCrystal structure of Thermus thermophilus FakA ATP-binding domain
ComponentsProbable kinase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid kinase / ATP-binding protein / Lipid metabolism / phosphotransferase
Function / homology
Function and homology information


glycerone kinase activity / glycerol metabolic process / phosphorylation
Similarity search - Function
DAK2 domain-containing protein YloV / Uncharacterised protein, DhaK domain / Fatty acid kinase subunit A-like, C-terminal / Dak1_2 / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Probable kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92850331296 Å
AuthorsNakatani, M. / Nakahara, S. / Fukui, K. / Murakawa, T. / Masui, R.
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Crystal structure of a nucleotide-binding domain of fatty acid kinase FakA from Thermus thermophilus HB8.
Authors: Nakatani, M. / Nakahara, S.Y. / Fukui, K. / Urano, M. / Fujii, Y. / Murakawa, T. / Baba, S. / Kumasaka, T. / Okanishi, H. / Kanai, Y. / Yano, T. / Masui, R.
History
DepositionMar 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable kinase
B: Probable kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0048
Polymers48,0522
Non-polymers9526
Water2,702150
1
A: Probable kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5024
Polymers24,0261
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-28 kcal/mol
Surface area9300 Å2
MethodPISA
2
B: Probable kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5024
Polymers24,0261
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-28 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.190, 90.190, 111.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21B-308-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 3 and (name O or name...A3 - 44
121(chain A and ((resid 3 and (name O or name...A46 - 62
131(chain A and ((resid 3 and (name O or name...A65 - 114
141(chain A and ((resid 3 and (name O or name...A116 - 119
151(chain A and ((resid 3 and (name O or name...A122 - 124
161(chain A and ((resid 3 and (name O or name...A126 - 158
171(chain A and ((resid 3 and (name O or name...A161 - 167
181(chain A and ((resid 3 and (name O or name...A169 - 173
191(chain A and ((resid 3 and (name O or name...A175 - 191
1101(chain A and ((resid 3 and (name O or name...A194 - 198
2111(chain B and (resseq 3 or (resid 4 and (name...B3 - 44
2121(chain B and (resseq 3 or (resid 4 and (name...B46 - 62
2131(chain B and (resseq 3 or (resid 4 and (name...B65 - 114
2141(chain B and (resseq 3 or (resid 4 and (name...B116 - 119
2151(chain B and (resseq 3 or (resid 4 and (name...B122 - 124
2161(chain B and (resseq 3 or (resid 4 and (name...B126 - 158
2171(chain B and (resseq 3 or (resid 4 and (name...B161 - 167
2181(chain B and (resseq 3 or (resid 4 and (name...B169 - 173
2191(chain B and (resseq 3 or (resid 4 and (name...B175 - 191
2201(chain B and (resseq 3 or (resid 4 and (name...B194 - 198

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Components

#1: Protein Probable kinase / FakA


Mass: 24026.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: TTHA0214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLS9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M sodium chloride, 0.1M tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.928→45.095 Å / Num. obs: 35300 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 31.9281053418 Å2 / CC1/2: 0.999 / Net I/σ(I): 13
Reflection shellResolution: 1.928→2 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 3455 / CC1/2: 0.671 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155model building
Cootv0.7.2model building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.92850331296→45.095 Å / SU ML: 0.235269670355 / Cross valid method: FREE R-VALUE / σ(F): 1.35596896543 / Phase error: 26.3801595096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236411716719 1761 4.99971608654 %
Rwork0.208022978316 33461 -
obs0.20945075519 35222 99.6407253388 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.5712042685 Å2
Refinement stepCycle: LAST / Resolution: 1.92850331296→45.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 58 150 3136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003391946839453037
X-RAY DIFFRACTIONf_angle_d0.7525195763874130
X-RAY DIFFRACTIONf_chiral_restr0.0398264447893469
X-RAY DIFFRACTIONf_plane_restr0.00381801148787536
X-RAY DIFFRACTIONf_dihedral_angle_d14.71310772781799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92851-1.98060.3296491281261300.339040526032483X-RAY DIFFRACTION98.7901701323
1.9806-2.03890.3475917835831340.3048091743192529X-RAY DIFFRACTION99.514200299
2.0389-2.10470.2777638136321330.2580712771692538X-RAY DIFFRACTION99.7386109037
2.1047-2.180.2632494173881320.2453519211012537X-RAY DIFFRACTION99.6639283047
2.18-2.26720.3000588335761340.2432217887962538X-RAY DIFFRACTION99.6271439224
2.2672-2.37040.2489267946761340.2253840196862545X-RAY DIFFRACTION99.6281145407
2.3704-2.49540.276117928621340.2157364198892541X-RAY DIFFRACTION99.8134328358
2.4954-2.65170.2561176539221360.2112202767862573X-RAY DIFFRACTION99.5955882353
2.6517-2.85640.2705837883391340.2141320318972543X-RAY DIFFRACTION99.6278377373
2.8564-3.14380.2419139380421370.2130307486852593X-RAY DIFFRACTION99.8171846435
3.1438-3.59860.2306503418421370.1954028209732614X-RAY DIFFRACTION99.8185776488
3.5986-4.53310.2043458481251390.1687659688392641X-RAY DIFFRACTION99.892202659
4.5331-45.0940.194539354941470.1919828235422786X-RAY DIFFRACTION99.7958489282
Refinement TLS params.Method: refined / Origin x: 65.6003758771 Å / Origin y: 23.9573740345 Å / Origin z: 55.167669126 Å
111213212223313233
T0.274808714771 Å2-0.0505659824992 Å20.0050419522482 Å2-0.238568350436 Å20.0200006575873 Å2--0.260371036362 Å2
L1.00294147705 °20.483937943238 °20.311888787731 °2-1.21711950012 °20.868744022224 °2--2.68104729803 °2
S0.125317948428 Å °-0.123025871989 Å °-0.0879136075103 Å °0.241533379341 Å °-0.174598471846 Å °0.0566401276011 Å °0.448256097603 Å °-0.43541275648 Å °0.0443119000731 Å °
Refinement TLS groupSelection details: all

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