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- PDB-1gjv: Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) complxed... -

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Basic information

Entry
Database: PDB / ID: 1gjv
TitleBranched-chain alpha-ketoacid dehydrogenase kinase (BCK) complxed with ATP-gamma-S
Components[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE
KeywordsTRANSFERASE / MITOCHONDRIAL PROTEIN KINASE / POTASSIUM
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / regulation of glucose metabolic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding
Similarity search - Function
Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain ...Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMachius, M. / Chuang, J.L. / Wynn, M.R. / Tomchick, D.R. / Chuang, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of Rat Bckd Kinase: Nucleotide-Induced Domain Communication in a Mitochondrial Protein Kinase.
Authors: Machius, M. / Chuang, J.L. / Wynn, M.R. / Tomchick, D.R. / Chuang, D.T.
History
DepositionAug 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0259
Polymers44,2621
Non-polymers7648
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)127.722, 127.722, 74.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein [3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE / BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE


Mass: 44261.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HIS6-TAG / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PTRCKINASEHIS6/PGROESL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CG-712 / References: UniProt: Q00972, EC: 2.7.1.115

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Non-polymers , 5 types, 78 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCRYSTALLIZED VERSION CONTAINS A C-TERMINAL HIS6-TAG

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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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: VAPOR DIFFUSION 20C EQUAL AMOUNTS OF BCK (20 MG/ML IN 50 MM HEPES PH 7.5, 1 M SODIUM CHLORIDE,250 MM POTASSIUM CHLORIDE, 300 MM ARGININE, 20 MM BETA-MERCAPTOETHANOL 2 MM BENZAMIDINE, 2 MM MG- ...Details: VAPOR DIFFUSION 20C EQUAL AMOUNTS OF BCK (20 MG/ML IN 50 MM HEPES PH 7.5, 1 M SODIUM CHLORIDE,250 MM POTASSIUM CHLORIDE, 300 MM ARGININE, 20 MM BETA-MERCAPTOETHANOL 2 MM BENZAMIDINE, 2 MM MG-ATPGAMMAS, 2 MM MAGNESIUM CHLORIDE, 0.5 MM PMSF, 10% (W/V) GLYCEROL) AND RESERVOIR (8%(W/V) PEG-6000, 5% (V/V) ETHYLENE GLYCOL, 1 M NACL, 20 MM BETA-MERCAPTOETHANOL)
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMHEPES1drop
31 M1dropNaCl
4250 mM1dropKCl
5300 mMarginine1drop
620 mMbeta-mercaptoethanol1drop
71 mMbenzamidine1drop
82 mM1dropMgCl2
90.5 mMPMSF1drop
1010 %(v/v)glycerol1drop
128 %(w/v)PEG60001reservoir
135 %(v/v)ethylene glycol1reservoir
141 M1reservoirNaCl
1520 mMbeta-mercaptoethanol1reservoir
11ATP gammaS1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MSC / Detector: IMAGE PLATE / Date: Apr 15, 2001 / Details: OSMIC MIRROR SYSTEM
RadiationMonochromator: OSMIC MIRROR SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→36.9 Å / Num. obs: 17401 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2 / % possible all: 96.8
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.582

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE (BCK) SELENOMETHIONINE VARIANT

Resolution: 2.7→36.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 298048.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REGIONS: 1-37, 307-335, 379-388 WERE NOT SEEN IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1430 8.6 %RANDOM
Rwork0.218 ---
obs0.218 16665 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.4908 Å2 / ksol: 0.354628 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å20 Å2
2--2.71 Å20 Å2
3----5.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 38 70 2634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 207 8.5 %
Rwork0.347 2240 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ION.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4MY_ATP-CAB.PARAM&_1_TOPOLOGY_INFILE_4
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.231 / Rfactor Rwork: 0.281
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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