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- PDB-3ju5: Crystal Structure of Dimeric Arginine Kinase at 1.75-A Resolution -

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Basic information

Entry
Database: PDB / ID: 3ju5
TitleCrystal Structure of Dimeric Arginine Kinase at 1.75-A Resolution
ComponentsArginine kinase
KeywordsTRANSFERASE / arginine kinase / reciprocating mechanism / negative cooperativity / phosphagen kinase / ATP-binding / Kinase / Nucleotide-binding
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / 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 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 speciesApostichopus japonicus (Japanese sea cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsWu, X. / Ye, S. / Guo, S. / Yan, W. / Bartlam, M. / Rao, Z.
CitationJournal: Faseb J. / Year: 2010
Title: Structural basis for a reciprocating mechanism of negative cooperativity in dimeric phosphagen kinase activity
Authors: Wu, X. / Ye, S. / Guo, S. / Yan, W. / Bartlam, M. / Rao, Z.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine kinase
B: Arginine kinase
C: Arginine kinase
D: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,1386
Polymers171,0904
Non-polymers492
Water30,8241711
1
A: Arginine kinase
B: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5693
Polymers85,5452
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-10 kcal/mol
Surface area30970 Å2
MethodPISA
2
C: Arginine kinase
D: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5693
Polymers85,5452
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-8 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.881, 59.868, 139.873
Angle α, β, γ (deg.)90.00, 92.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arginine kinase / / AK


Mass: 42772.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apostichopus japonicus (Japanese sea cucumber)
Gene: AK / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9XY07, arginine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1711 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M Bis-Tris (pH 6.6), 12% PEG 1000, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→86.7 Å / Num. all: 134595 / Num. obs: 132173 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.68 / Num. unique all: 11065 / % possible all: 85.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→75.34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.442 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22671 7021 5 %RANDOM
Rwork0.16997 ---
obs0.17282 132173 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.499 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→75.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11671 0 2 1711 13384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02211898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.96415998
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23551477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6924.206573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.152152270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2271584
X-RAY DIFFRACTIONr_chiral_restr0.1480.21729
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218940
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2441.57261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.994211710
X-RAY DIFFRACTIONr_scbond_it3.39234637
X-RAY DIFFRACTIONr_scangle_it5.3074.54274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 410 -
Rwork0.237 7689 -
obs--76.43 %

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