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- PDB-1crk: MITOCHONDRIAL CREATINE KINASE -

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Basic information

Entry
Database: PDB / ID: 1crk
TitleMITOCHONDRIAL CREATINE KINASE
ComponentsCREATINE KINASE
KeywordsTRANSFERASE / CREATINE KINASE
Function / homology
Function and homology information


creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / mitochondrial inner membrane / 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
PHOSPHATE ION / Creatine kinase S-type, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SIR, PHASEEXTENS / Resolution: 3 Å
AuthorsFritz-Wolf, K. / Schnyder, T. / Wallimann, T. / Kabsch, W.
CitationJournal: Nature / Year: 1996
Title: Structure of mitochondrial creatine kinase.
Authors: Fritz-Wolf, K. / Schnyder, T. / Wallimann, T. / Kabsch, W.
History
DepositionMar 8, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: CREATINE KINASE
B: CREATINE KINASE
C: CREATINE KINASE
D: CREATINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,79712
Polymers173,0384
Non-polymers7608
Water0
1
A: CREATINE KINASE
B: CREATINE KINASE
C: CREATINE KINASE
D: CREATINE KINASE
hetero molecules

A: CREATINE KINASE
B: CREATINE KINASE
C: CREATINE KINASE
D: CREATINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,59524
Polymers346,0758
Non-polymers1,52016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)126.000, 126.000, 144.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
CREATINE KINASE /


Mass: 43259.418 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: SARCOMER / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle / References: UniProt: P11009, creatine kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %PEG10001reservoir
225 mMsodium phosphate1reservoir
31 mM1reservoirNaN3
42 mMbeta-mercaptoethanol1reservoir
50.2 mMNa2 EDTA1reservoir
62.5 mg/mlprotein1drop
78.5 %PEG10001drop
825 mMsodium phosphate1drop
91 mM1dropNaN3
102 mMbeta-mercaptoethanol1drop
110.2 mMNa2 EDTA1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 27, 1993 / Details: FRANKS DOUBLE MIRROR OPTICS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 45021 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.84
Reflection shellResolution: 3→3.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.32 / % possible all: 99

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Processing

Software
NameClassification
MIRmodel building
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: SIR, PHASEEXTENS / Resolution: 3→8 Å / σ(F): 0
Details: DISORDERED RESIDUES 1 - 5, 318 - 326 WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.264 -10 %
Rwork0.217 --
obs0.217 40730 99.6 %
Displacement parametersBiso mean: 37.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 40 0 12184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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