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- PDB-2crk: MUSCLE CREATINE KINASE -

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Basic information

Entry
Database: PDB / ID: 2crk
TitleMUSCLE CREATINE KINASE
ComponentsPROTEIN (CREATINE KINASE)
KeywordsTRANSFERASE / CREATINE KINASE
Function / homology
Function and homology information


creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / response to heat / 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 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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.35 Å
AuthorsRao, J.K. / Bujacz, G. / Wlodawer, A.
CitationJournal: FEBS Lett. / Year: 1998
Title: Crystal structure of rabbit muscle creatine kinase.
Authors: Rao, J.K. / Bujacz, G. / Wlodawer, A.
History
DepositionSep 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CREATINE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6855
Polymers43,3011
Non-polymers3844
Water7,764431
1
A: PROTEIN (CREATINE KINASE)
hetero molecules

A: PROTEIN (CREATINE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,37110
Polymers86,6022
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)199.600, 199.600, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein PROTEIN (CREATINE KINASE)


Mass: 43301.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00563, creatine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 4.2 Å3/Da / Density % sol: 68 %
Crystal growpH: 7.2
Details: 55% TO 60% SATURATED AMMONIUM SULFATE, 2.5% PEG400 IN HEPES BUFFER AT PH 7.2, ABOUT 5MM/MG PROTEIN CONCENTRATION
Crystal
*PLUS
Crystal grow
*PLUS
Method: standing drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
250 mMNa-HEPES1drop
355 %satammonium sulfate1reservoir
42.5 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: FRANKS DOUBLE MIRROR OPTICS
RadiationMonochromator: PT AND NI COATED GLASS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 29042 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 9.4 % / Rsym value: 0.101 / Net I/σ(I): 16.45
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.78 / Rsym value: 0.339 / % possible all: 89.2
Reflection
*PLUS
Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
PHASESphasing
AMoREphasing
MADIRA(UNPUBLISHED)model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
MADIRA(UNPUBLISHED)phasing
RefinementMethod to determine structure: MIR
Starting model: 1CRK

1crk


Resolution: 2.35→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 -9 %RANDOM
Rwork0.195 ---
obs0.195 27515 96.5 %-
Displacement parametersBiso mean: 26.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.35→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 20 431 3380
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.285 9 %
Rwork0.377 -
obs-89 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / σ(F): 2 / Num. reflection Rfree: 2943 / % reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / % reflection Rfree: 9 % / Rfactor Rwork: 0.377

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