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- PDB-4woe: The duplicated taurocyamine kinase from Schistosoma mansoni with ... -

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Basic information

Entry
Database: PDB / ID: 4woe
TitleThe duplicated taurocyamine kinase from Schistosoma mansoni with bound transition state analog (TSA) components
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
Taurocyamine / ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / Taurocyamine kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)163,42015
Polymers160,8452
Non-polymers2,57413
Water13,313739
1
A: Taurocyamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7849
Polymers80,4231
Non-polymers1,3618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Taurocyamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6366
Polymers80,4231
Non-polymers1,2135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.695, 122.220, 63.060
Angle α, β, γ (deg.)90.00, 108.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 80422.703 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 752 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-3S5 / Taurocyamine / 2-carbamimidamidoethanesulfonic acid


Mass: 167.187 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9N3O3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 68919 / Num. obs: 67921 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rsym value: 0.128 / Net I/σ(I): 7.18
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.26 / Rsym value: 0.442 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WO8

4wo8


Resolution: 2.3→46.74 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 3394 5 %Random selection
Rwork0.1855 ---
obs0.1891 67921 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11154 0 159 739 12052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911537
X-RAY DIFFRACTIONf_angle_d1.21115585
X-RAY DIFFRACTIONf_dihedral_angle_d15.3814343
X-RAY DIFFRACTIONf_chiral_restr0.0431702
X-RAY DIFFRACTIONf_plane_restr0.0051996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33290.35841360.24712591X-RAY DIFFRACTION95
2.3329-2.36770.29291380.23132632X-RAY DIFFRACTION98
2.3677-2.40470.33151440.21822719X-RAY DIFFRACTION100
2.4047-2.44410.26351420.20042698X-RAY DIFFRACTION100
2.4441-2.48620.26631410.20232697X-RAY DIFFRACTION100
2.4862-2.53150.30291450.19312745X-RAY DIFFRACTION100
2.5315-2.58010.29881410.19662677X-RAY DIFFRACTION100
2.5801-2.63280.30311430.19052723X-RAY DIFFRACTION100
2.6328-2.690.26711410.1892684X-RAY DIFFRACTION100
2.69-2.75260.29281450.19492742X-RAY DIFFRACTION100
2.7526-2.82140.29621410.19512693X-RAY DIFFRACTION100
2.8214-2.89770.26761420.19982683X-RAY DIFFRACTION100
2.8977-2.9830.26091440.18992735X-RAY DIFFRACTION99
2.983-3.07920.28291410.18932677X-RAY DIFFRACTION99
3.0792-3.18930.25721430.19492722X-RAY DIFFRACTION99
3.1893-3.31690.28871420.18642708X-RAY DIFFRACTION99
3.3169-3.46780.23381420.182689X-RAY DIFFRACTION99
3.4678-3.65060.21491390.1722647X-RAY DIFFRACTION98
3.6506-3.87920.24931400.16712647X-RAY DIFFRACTION97
3.8792-4.17860.22751420.1622697X-RAY DIFFRACTION98
4.1786-4.59870.1951390.15292660X-RAY DIFFRACTION97
4.5987-5.26340.20371410.16092671X-RAY DIFFRACTION97
5.2634-6.62830.24411420.19982687X-RAY DIFFRACTION98
6.6283-46.74980.25761400.19642659X-RAY DIFFRACTION95

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