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- PDB-7ed9: Crystal structure of selenomethionine-labeled Thermus thermophilu... -

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Basic information

Entry
Database: PDB / ID: 7ed9
TitleCrystal structure of selenomethionine-labeled 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 / MOLECULAR REPLACEMENT / Resolution: 2.01764160944 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)48,3478
Polymers47,3962
Non-polymers9526
Water1,946108
1
A: Probable kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1744
Polymers23,6981
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-28 kcal/mol
Surface area8850 Å2
MethodPISA
2
B: Probable kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1744
Polymers23,6981
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-28 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.740, 90.740, 112.600
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-304-

HOH

21B-301-

HOH

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

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAMETMET(chain A and (resseq 4:11 or (resid 12 and (name...AA4 - 6425 - 85
12GLNGLNLEULEU(chain A and (resseq 4:11 or (resid 12 and (name...AA66 - 9187 - 112
13GLYGLYSERSER(chain A and (resseq 4:11 or (resid 12 and (name...AA93 - 119114 - 140
14LYSLYSALAALA(chain A and (resseq 4:11 or (resid 12 and (name...AA122 - 158143 - 179
15GLUGLULEULEU(chain A and (resseq 4:11 or (resid 12 and (name...AA161 - 163182 - 184
16THRTHRPROPRO(chain A and (resseq 4:11 or (resid 12 and (name...AA166 - 167187 - 188
17LEULEULEULEU(chain A and (resseq 4:11 or (resid 12 and (name...AA169 - 173190 - 194
18GLNGLNLEULEU(chain A and (resseq 4:11 or (resid 12 and (name...AA175 - 198196 - 219
29ALAALAMETMET(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB4 - 6425 - 85
210GLNGLNLEULEU(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB66 - 9187 - 112
211GLYGLYSERSER(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB93 - 119114 - 140
212LYSLYSALAALA(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB122 - 158143 - 179
213GLUGLULEULEU(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB161 - 163182 - 184
214THRTHRPROPRO(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB166 - 167187 - 188
215LEULEULEULEU(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB169 - 173190 - 194
216GLNGLNLEULEU(chain B and (resseq 4:64 or resseq 66:91 or resseq...BB175 - 198196 - 219

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Components

#1: Protein Probable kinase / FakA


Mass: 23697.781 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-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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M sodium chloride, 0.1M tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.0176→47.939 Å / Num. obs: 31444 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 35.9817979205 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 1.18 / Num. unique obs: 3068 / CC1/2: 0.765 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155model building
Coot0.7.2model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ED6

7ed6


Resolution: 2.01764160944→47.8397910997 Å / SU ML: 0.260464862152 / Cross valid method: FREE R-VALUE / σ(F): 1.3434917436 / Phase error: 25.8674484197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247934236065 1568 4.98664292075 %
Rwork0.226847345998 29876 -
obs0.227919186825 31444 99.5378284267 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.0891061531 Å2
Refinement stepCycle: LAST / Resolution: 2.01764160944→47.8397910997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 58 108 3058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002270378278982999
X-RAY DIFFRACTIONf_angle_d0.6579774836114077
X-RAY DIFFRACTIONf_chiral_restr0.0365539563146466
X-RAY DIFFRACTIONf_plane_restr0.0037196713034527
X-RAY DIFFRACTIONf_dihedral_angle_d16.02058661061783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01765-2.08280.3371528258351360.3514127176362617X-RAY DIFFRACTION98.5325697924
2.0828-2.15720.3334673568581390.3092655322162677X-RAY DIFFRACTION99.3648553282
2.1572-2.24360.2955786790841400.2927995029882650X-RAY DIFFRACTION99.7140814868
2.2436-2.34570.2953994571471400.2586805829712669X-RAY DIFFRACTION99.0130419457
2.3457-2.46930.2962579366291430.2516165288592687X-RAY DIFFRACTION99.61281239
2.4693-2.6240.2543685550581400.2418423883692686X-RAY DIFFRACTION99.6473906911
2.624-2.82660.3095089502751420.2480420106142714X-RAY DIFFRACTION99.6510816469
2.8266-3.1110.2415238979721430.2352780812842714X-RAY DIFFRACTION99.7904296193
3.111-3.56110.2261358212051440.2175311543662749X-RAY DIFFRACTION99.8619261305
3.5611-4.48610.2087743969291470.1901746567282776X-RAY DIFFRACTION99.9316239316
4.4861-47.8390.2280143974171540.2006260236622937X-RAY DIFFRACTION99.8062641266
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8375640022910.8860571582670.01591516831461.029191108350.1976577276331.825464928830.03335314224720.0223747483279-0.04399819724610.120326754215-0.02826910047820.0202575486250.294738896405-0.0598331969493-9.88692537502E-50.3154957282610.01451117857070.001018923255370.245591204816-0.01882397920760.29165895093923.9711418508-24.8700767066-13.0311040699
20.7861474987851.050463606320.2788498408561.569027863440.6258276881112.225402747180.130865279487-0.151759959281-0.002765793609280.148217115602-0.1789319218560.01381084437620.27139665587-0.392157619604-0.007676082808260.284762793796-0.07769692449830.03510005103170.3401183597-0.01042801428320.30189913701516.4332831728-17.201503558313.1999575915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq -1:198)
2X-RAY DIFFRACTION2(chain B and resseq 4:198)

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