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- PDB-1qk1: CRYSTAL STRUCTURE OF HUMAN UBIQUITOUS MITOCHONDRIAL CREATINE KINASE -

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Basic information

Entry
Database: PDB / ID: 1qk1
TitleCRYSTAL STRUCTURE OF HUMAN UBIQUITOUS MITOCHONDRIAL CREATINE KINASE
ComponentsCREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
KeywordsTRANSFERASE (CREATINE KINASE) / MITOCHONDRIAL CREATINE KINASE / CANCER / CELLULAR ENERGY METABOLISM / GUANIDINO KINASE / MITOCHONDRIAL PERMEABILITY TRANSITION / OCTAMER STABILITY
Function / homology
Function and homology information


creatine kinase / creatine metabolic process / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / kinase activity / mitochondrial inner membrane / 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 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 U-type, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEder, M. / Schlattner, U. / Fritz-Wolf, K. / Wallimann, T. / Kabsch, W.
Citation
Journal: Proteins: Struct.,Funct., Genet. / Year: 2000
Title: Crystal Structure of Human Ubiquitous Mitochondrial Creatine Kinase
Authors: Eder, M. / Fritz-Wolf, K. / Kabsch, W. / Wallimann, T. / Schlattner, U.
#1: Journal: Nature / Year: 1996
Title: Structure of Mitochondrial Creatine Kinase:
Authors: Fritz-Wolf, K. / Schnyder, T. / Wallimann, T. / Kabsch, W.
History
DepositionJul 8, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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, UBIQUITOUS MITOCHONDRIAL
B: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
C: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
D: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
E: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
F: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
G: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
H: CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,48816
Polymers345,7298
Non-polymers7608
Water5,278293
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28440 Å2
ΔGint38.6 kcal/mol
Surface area154720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.811, 125.868, 212.074
Angle α, β, γ (deg.)90.00, 96.71, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE MOLECULE EXISTS AS AN OCTAMER COMPOSED OFFOUR UMTCK HOMODIMERS.

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Components

#1: Protein
CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL / / UMTCK / MIA-CK


Mass: 43216.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: RECOMBINANT HUMAN UMTCK HAS AN ADDITIONAL ALA AT THE N-TERMINUS
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLACENTA
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Gene: GENBANK ACCESSION J04469 GENE: GENBANK ACCESSION J04469
Plasmid: PUS04 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P12532, creatine kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Source detailsFOR THE MIA-CK STUDIED HERE THE MATURE PROTEIN SEQUENCE STARTS AT POSITION 39 OF THE PRECURSOR ...FOR THE MIA-CK STUDIED HERE THE MATURE PROTEIN SEQUENCE STARTS AT POSITION 39 OF THE PRECURSOR PROTEIN. THE SWS P12532 STARTS AT 40, WITH RESIDUES 1 39 MITOCHONDRION (TRANSIT) 40 417 CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL THEREFORE AN ADDITIONAL ALA IS PRESENT AT THE N-TERMINUS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 6.75
Details: 0.025M NA-PHOSPHATE, 3 MM DTT, PH 6.75, 5 MG/ML PROTEIN
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMsodium phosphate11
22 mMbeta-mercaptoethanol11
30.2 mMEDTA11
45 mg/mlprotein11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: MULTIWIRE SIEMENS / Detector: AREA DETECTOR / Date: Dec 15, 1998 / Details: FRANKS DOUBLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 130945 / % possible obs: 99.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 616668
Reflection shell
*PLUS
% possible obs: 99.1 % / Num. unique obs: 13429 / Num. measured obs: 43256

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Processing

Software
NameVersionClassification
CNS0.5refinement
XDSV. 99data reduction
XDSV. 99data scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CRK, SARCOMERIC MITOCHONDRIAL CREATINE KINASE

1crk


Resolution: 2.7→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R-VALUE / σ(F): 0
Details: DISORDERED RESIDUES 316-325 AND 375- 379 (CHAIN A-H) WERE MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6548 5 %RANDOM
Rwork0.195 ---
obs0.195 130945 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.97 Å2 / ksol: 0.2798 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.16 Å20 Å20.63 Å2
2---1.59 Å20 Å2
3----5.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24280 0 40 293 24613
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 649 5 %
Rwork0.277 12324 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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