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- PDB-4wo8: The substrate-free duplicated taurocyamine kinase from Schistosom... -

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Basic information

Entry
Database: PDB / ID: 4wo8
TitleThe substrate-free duplicated taurocyamine kinase from Schistosoma mansoni
ComponentsTaurocyamine kinase
KeywordsTRANSFERASE / duplicated / substrate specificity / transition state
Function / homology
Function and homology information


taurocyamine kinase / taurocyamine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / oxidoreductase activity / extracellular space / ATP binding / metal ion binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMerceron, R. / Awama, A. / Montserret, R. / Marcillat, O. / Gouet, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Substrate-free and -bound Crystal Structures of the Duplicated Taurocyamine Kinase from the Human Parasite Schistosoma mansoni.
Authors: Merceron, R. / Awama, A.M. / Montserret, R. / Marcillat, O. / Gouet, P.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Taurocyamine kinase


Theoretical massNumber of molelcules
Total (without water)80,4231
Polymers80,4231
Non-polymers00
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.840, 122.020, 62.970
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Taurocyamine kinase / ATP:guanidino kinase Smc74 / ATP:guanidino phosphotransferase / SmGK


Mass: 80422.703 Da / Num. of mol.: 1 / Fragment: UNP residues 31-746 / Mutation: A11V D235G I237T D493G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_194770 / Production host: Escherichia coli (E. coli) / References: UniProt: P16641, taurocyamine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 200 mM ammonium tartrate dibasic pH 5.4, 20% (w/v) polyethylene glycol 3350, 20% (v/v) ethylene glycol
PH range: 5.4 - 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 38515 / Num. obs: 38030 / % possible obs: 98.7 % / Redundancy: 3.1 % / Net I/σ(I): 11.71
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.11 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j1q

2j1q


Resolution: 2.2→46.182 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1900 5 %Random selection
Rwork0.1763 ---
obs0.1786 38011 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 0 362 5930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085680
X-RAY DIFFRACTIONf_angle_d1.1757662
X-RAY DIFFRACTIONf_dihedral_angle_d14.0562139
X-RAY DIFFRACTIONf_chiral_restr0.043842
X-RAY DIFFRACTIONf_plane_restr0.006991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25510.31291310.29492513X-RAY DIFFRACTION97
2.2551-2.3160.27591360.22382579X-RAY DIFFRACTION99
2.316-2.38420.23241350.19932577X-RAY DIFFRACTION100
2.3842-2.46110.24371370.18462601X-RAY DIFFRACTION100
2.4611-2.54910.25911380.19142617X-RAY DIFFRACTION100
2.5491-2.65110.23471370.18522598X-RAY DIFFRACTION100
2.6511-2.77180.2671360.19122595X-RAY DIFFRACTION100
2.7718-2.91790.28821360.18812578X-RAY DIFFRACTION100
2.9179-3.10070.22571370.19172610X-RAY DIFFRACTION100
3.1007-3.340.21691360.17652578X-RAY DIFFRACTION99
3.34-3.6760.22081350.16562557X-RAY DIFFRACTION98
3.676-4.20760.2051330.15512539X-RAY DIFFRACTION97
4.2076-5.29990.17671360.14292577X-RAY DIFFRACTION98
5.2999-46.1920.19341370.16132592X-RAY DIFFRACTION98

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