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- PDB-1i0e: CRYSTAL STRUCTURE OF CREATINE KINASE FROM HUMAN MUSCLE -

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Basic information

Entry
Database: PDB / ID: 1i0e
TitleCRYSTAL STRUCTURE OF CREATINE KINASE FROM HUMAN MUSCLE
ComponentsCREATINE KINASE,M CHAIN
KeywordsTRANSFERASE / Double helix / dimer
Function / homology
Function and homology information


creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / extracellular space / ATP binding / cytosol
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
Creatine kinase M-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsShen, Y.-Q. / Tang, L. / Zhou, H.-M. / Lin, Z.-J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of human muscle creatine kinase.
Authors: Shen, Y.Q. / Tang, L. / Zhou, H.M. / Lin, Z.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray analysis of human muscle creatine kinase.
Authors: Tang, L. / Zhou, H.-M. / Lin, Z.-J.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREATINE KINASE,M CHAIN
B: CREATINE KINASE,M CHAIN
C: CREATINE KINASE,M CHAIN
D: CREATINE KINASE,M CHAIN


Theoretical massNumber of molelcules
Total (without water)172,6814
Polymers172,6814
Non-polymers00
Water0
1
A: CREATINE KINASE,M CHAIN

A: CREATINE KINASE,M CHAIN


Theoretical massNumber of molelcules
Total (without water)86,3402
Polymers86,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,x-y+1,-z+11
2
B: CREATINE KINASE,M CHAIN

B: CREATINE KINASE,M CHAIN


Theoretical massNumber of molelcules
Total (without water)86,3402
Polymers86,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557x,x-y,-z+21
3
C: CREATINE KINASE,M CHAIN

D: CREATINE KINASE,M CHAIN


Theoretical massNumber of molelcules
Total (without water)86,3402
Polymers86,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,x-y+1,-z+11
4
C: CREATINE KINASE,M CHAIN

D: CREATINE KINASE,M CHAIN


Theoretical massNumber of molelcules
Total (without water)86,3402
Polymers86,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation6_566x,x-y+1,-z+11
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.326, 89.326, 402.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein
CREATINE KINASE,M CHAIN


Mass: 43170.137 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: MUSCLESkeletal muscle / References: UniProt: P06732, creatine kinase

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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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 5.8 / Details: Tang, L., (1998) Acta Crystallogr., D55, 669.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1droppH5.8
240 %MPD1drop
340 %MPD1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 21262 / % possible obs: 0.883 % / Redundancy: 3 % / Biso Wilson estimate: 24.347 Å2 / Rmerge(I) obs: 0.118
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2 / Num. unique all: 2232 / % possible all: 0.935
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 63933
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rabbit muscle creatine kinase

Resolution: 3.5→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4033176.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1915 9.8 %RANDOM
Rwork0.211 ---
obs0.211 19482 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 107.8 Å2 / ksol: 0.451 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å29.85 Å20 Å2
2--0.79 Å20 Å2
3----1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11608 0 0 0 11608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.83
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 319 9.4 %
Rwork0.266 3061 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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