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- PDB-3l2d: Glycocyamine kinase, beta-beta homodimer from marine worm Namalyc... -

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Basic information

Entry
Database: PDB / ID: 3l2d
TitleGlycocyamine kinase, beta-beta homodimer from marine worm Namalycastis sp.
ComponentsGlycocyamine kinase beta chain
KeywordsTRANSFERASE / phosphagen kinase / glycocyamine kinase / Kinase
Function / homology
Function and homology information


phosphocreatine biosynthetic process / creatine kinase activity / mitochondrion / 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
Similarity search - Component
Biological speciesNamalycastis sp. ST01 (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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

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Assembly

Deposited unit
A: Glycocyamine kinase beta chain
B: Glycocyamine kinase beta chain
C: Glycocyamine kinase beta chain
D: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)176,4334
Polymers176,4334
Non-polymers00
Water11,223623
1
A: Glycocyamine kinase beta chain
B: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)88,2172
Polymers88,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycocyamine kinase beta chain
D: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)88,2172
Polymers88,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glycocyamine kinase beta chain

D: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)88,2172
Polymers88,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1980 Å2
ΔGint-7 kcal/mol
Surface area33230 Å2
MethodPISA
4
B: Glycocyamine kinase beta chain
C: Glycocyamine kinase beta chain


Theoretical massNumber of molelcules
Total (without water)88,2172
Polymers88,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-8 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.62, 99.72, 93.30
Angle α, β, γ (deg.)90.00, 92.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycocyamine kinase beta chain


Mass: 44108.363 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 60423 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.5 / % possible all: 99.4

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Processing

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

1qh4


Resolution: 2.4→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 3038 random
Rwork0.197 --
obs-60171 -
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11830 0 0 623 12453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree: 0.341 / Rfactor Rwork: 0.276

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