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- PDB-4wod: The duplicated taurocyamine kinase from Schistosoma mansoni compl... -

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Basic information

Entry
Database: PDB / ID: 4wod
TitleThe duplicated taurocyamine kinase from Schistosoma mansoni complexed with arginine
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
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
Similarity search - Domain/homology
ARGININE / Taurocyamine kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Nov 21, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value ..._reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rsym_value
Revision 1.3Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5982
Polymers80,4231
Non-polymers1751
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 123.070, 62.740
Angle α, β, γ (deg.)90.00, 108.07, 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: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM ammonium tartrate dibasic pH 5.4, 20% (w/v) polyethylene glycol 3350, 20% (v/v) ethylene glycol, 5 mM L-Arginine
PH range: 5.4 - 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 58922 / Num. obs: 58275 / % possible obs: 98.9 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rsym value: 0.106 / Net I/σ(I): 12.11
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.41 / CC1/2: 0.892 / Rsym value: 0.456 / % possible all: 96.2

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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: 4WO8

4wo8


Resolution: 1.9→45.813 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2914 5 %Random selection
Rwork0.2056 ---
obs0.2079 58275 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 12 340 5920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085691
X-RAY DIFFRACTIONf_angle_d1.1067675
X-RAY DIFFRACTIONf_dihedral_angle_d14.6452145
X-RAY DIFFRACTIONf_chiral_restr0.043843
X-RAY DIFFRACTIONf_plane_restr0.005993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93110.29651310.29642502X-RAY DIFFRACTION94
1.9311-1.96440.34111390.29232630X-RAY DIFFRACTION100
1.9644-2.00020.35781410.29692671X-RAY DIFFRACTION100
2.0002-2.03860.35391370.30132618X-RAY DIFFRACTION100
2.0386-2.08020.39941390.29952644X-RAY DIFFRACTION99
2.0802-2.12550.30481390.27982623X-RAY DIFFRACTION99
2.1255-2.17490.34221380.28152626X-RAY DIFFRACTION99
2.1749-2.22930.30361360.26622597X-RAY DIFFRACTION98
2.2293-2.28960.30681370.25562603X-RAY DIFFRACTION99
2.2896-2.35690.32011410.24142675X-RAY DIFFRACTION99
2.3569-2.4330.26331380.22232615X-RAY DIFFRACTION99
2.433-2.520.29911410.21892671X-RAY DIFFRACTION99
2.52-2.62090.25941390.20142639X-RAY DIFFRACTION99
2.6209-2.74010.21211380.19432622X-RAY DIFFRACTION99
2.7401-2.88460.27411390.19382650X-RAY DIFFRACTION100
2.8846-3.06530.24241400.18172652X-RAY DIFFRACTION100
3.0653-3.30190.2261400.1812656X-RAY DIFFRACTION100
3.3019-3.6340.21471390.16982644X-RAY DIFFRACTION99
3.634-4.15960.19691400.16312670X-RAY DIFFRACTION100
4.1596-5.23940.17661400.15332663X-RAY DIFFRACTION99
5.2394-45.82620.22131420.19092674X-RAY DIFFRACTION99

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