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- PDB-1uf9: Crystal structure of TT1252 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1uf9
TitleCrystal structure of TT1252 from Thermus thermophilus
ComponentsTT1252 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / p-loop / nucleotide binding domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Dephospho-CoA kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSeto, A. / Murayama, K. / Toyama, M. / Ebihara, A. / Nakagawa, N. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: PROTEINS / Year: 2005
Title: ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8
Authors: Seto, A. / Murayama, K. / Toyama, M. / Ebihara, A. / Nakagawa, N. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TT1252 protein
B: TT1252 protein
C: TT1252 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1825
Polymers68,5793
Non-polymers6022
Water63135
1
A: TT1252 protein


Theoretical massNumber of molelcules
Total (without water)22,8601
Polymers22,8601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TT1252 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9552
Polymers22,8601
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TT1252 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3672
Polymers22,8601
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.120, 102.120, 65.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein TT1252 protein


Mass: 22859.820 Da / Num. of mol.: 3 / Fragment: nucleotide binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q56416
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.72M sodium citrate, 90mM imidazole, 10% PEG3000, 10mM CHES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMimidazole1reservoirpH8.0
220 mMCHES1reservoirpH9.5
30.8 Msodium citrate1reservoir
46 %PEG30001reservoir
52 mM1reservoirMgCl2
61 mMATP1reservoir
750 mMTris-HCl1droppH7.5
810 mMmagnesium acetatea1drop
920 mM1dropKCl
10100 mM1dropNaCl
110.2 mMATP1drop
120.2 mMdCoA1drop
131000 nm/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18914 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.7 Å2 / Rsym value: 0.093
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.298 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 159215 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.298

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→19.65 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1777090.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1846 9.8 %RANDOM
Rwork0.222 ---
obs-18811 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9993 Å2 / ksol: 0.306747 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å212.15 Å20 Å2
2--2.23 Å20 Å2
3----4.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 36 35 4607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d1.97
X-RAY DIFFRACTIONc_mcbond_it6.031.5
X-RAY DIFFRACTIONc_mcangle_it9.452
X-RAY DIFFRACTIONc_scbond_it9.852
X-RAY DIFFRACTIONc_scangle_it13.932.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 298 9.4 %
Rwork0.296 2876 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ATP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.2997 / Rfactor Rwork: 0.2222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.97

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