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- PDB-3l2e: Glycocyamine kinase, alpha-beta heterodimer from marine worm Nama... -

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Basic information

Entry
Database: PDB / ID: 3l2e
TitleGlycocyamine kinase, alpha-beta heterodimer from marine worm Namalycastis sp.
Components
  • Glycocyamine kinase alpha chain
  • Glycocyamine kinase beta chain
KeywordsTRANSFERASE / phosphagen kinase / glycocyamine kinase / Kinase
Function / homology
Function and homology information


phosphocreatine biosynthetic process / creatine kinase activity / extracellular space / ATP 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 / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. ...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 / 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
Glycocyamine kinase beta chain / Glycocyamine kinase alpha chain
Similarity search - Component
Biological speciesNamalycastis sp. ST01 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLim, K. / Pullalarevu, S. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 2010
Title: Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member.
Authors: Lim, K. / Pullalarevu, S. / Surabian, K.T. / Howard, A. / Suzuki, T. / Moult, J. / Herzberg, O.
#1: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 2005
Title: Isolation, characterization, and cDNA-derived amino acid sequence of glycocyamine kinase from the tropical marine worm Namalycastis sp.
Authors: Mizuta, C. / Tanaka, K. / Suzuki, T.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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: Glycocyamine kinase alpha chain
B: Glycocyamine kinase beta chain
C: Glycocyamine kinase alpha chain
D: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)173,3744
Polymers173,3744
Non-polymers00
Water4,828268
1
A: Glycocyamine kinase alpha chain
B: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)86,6872
Polymers86,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycocyamine kinase alpha chain
D: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)86,6872
Polymers86,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glycocyamine kinase alpha chain


Theoretical massNumber of molelcules
Total (without water)42,5791
Polymers42,5791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)44,1081
Polymers44,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Glycocyamine kinase alpha chain


Theoretical massNumber of molelcules
Total (without water)42,5791
Polymers42,5791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)44,1081
Polymers44,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.09, 98.20, 93.12
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycocyamine kinase alpha chain


Mass: 42578.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Namalycastis sp. ST01 (invertebrata) / Gene: GK-alpha, GK_alpha / Plasmid: pGK_alpha221 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: Q6AW43, EC: 2.7.3.1
#2: Protein Glycocyamine kinase beta chain


Mass: 44108.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Namalycastis sp. ST01 (invertebrata) / Gene: GK-beta, GK_beta / Plasmid: pGK_beta221 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: Q6AW42, EC: 2.7.3.1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% polyethylene glycol 3350, 0.2M sodium nitrate, 0.1M Tris HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 42293 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.7 / % possible all: 84.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QH4

1qh4


Resolution: 2.6→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 2118 random
Rwork0.192 --
obs-42274 -
Displacement parametersBiso mean: 52 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12031 0 0 268 12299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree: 0.371 / Rfactor Rwork: 0.293

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