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- PDB-3dre: Crystal structure of Human Brain-type Creatine Kinase -

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Basic information

Entry
Database: PDB / ID: 3dre
TitleCrystal structure of Human Brain-type Creatine Kinase
ComponentsCreatine kinase B-type
KeywordsTRANSFERASE / human / creatine kinase / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / RND3 GTPase cycle / substantia nigra development / phosphorylation / ubiquitin protein ligase binding / mitochondrion ...futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / RND3 GTPase cycle / substantia nigra development / phosphorylation / ubiquitin protein ligase binding / mitochondrion / extracellular space / extracellular exosome / ATP binding / plasma membrane / 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 B-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMoon, J.H. / Bong, S.M. / Hwang, K.Y. / Chi, Y.M.
CitationJournal: Febs Lett. / Year: 2008
Title: Structural studies of human brain-type creatine kinase complexed with the ADP-Mg2+-NO3- -creatine transition-state analogue complex
Authors: Bong, S.M. / Moon, J.H. / Nam, K.H. / Lee, K.S. / Chi, Y.M. / Hwang, K.Y.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Creatine kinase B-type
B: Creatine kinase B-type


Theoretical massNumber of molelcules
Total (without water)85,3982
Polymers85,3982
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.963, 97.963, 164.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Creatine kinase B-type / Creatine kinase B chain / B-CK


Mass: 42699.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12277, creatine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.31 Å3/Da / Density % sol: 46.71 % / Mosaicity: 0.508 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2007
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 41184 / Num. obs: 41184 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.135 / Χ2: 3.057 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.289.40.24340441.42399.5
2.28-2.37100.22640261.64199.7
2.37-2.4810.40.21340821.91799.8
2.48-2.6110.80.19840622.18599.8
2.61-2.7711.30.1840882.5599.8
2.77-2.9811.70.16340933.00799.7
2.98-3.28120.14641143.62199.9
3.28-3.7612.30.1341484.20199.5
3.76-4.7212.20.1241674.48599.1
4.72-2012.20.11243604.34398.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.69 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 65517 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2058 5 %RANDOM
Rwork0.205 ---
all0.225 41119 --
obs0.225 41119 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.806 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 93.56 Å2 / Biso mean: 37.654 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2--2.15 Å20 Å2
3----4.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 0 380 6269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it2.812
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_scangle_it4.062.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 351 5.2 %
Rwork0.227 6402 -
all-6753 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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