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- PDB-2a1h: X-ray crystal structure of human mitochondrial branched chain ami... -

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Basic information

Entry
Database: PDB / ID: 2a1h
TitleX-ray crystal structure of human mitochondrial branched chain aminotransferase (BCATm) complexed with gabapentin
Componentsbranched chain aminotransferase
KeywordsTRANSFERASE / FOLD TYPE IV
Function / homology
Function and homology information


regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism ...regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / amino acid biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal ...Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / [1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoto, M. / Miyahara, I. / Hirotsu, K. / Conway, M. / Yennawar, N. / Islam, M.M. / Hutson, S.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin.
Authors: Goto, M. / Miyahara, I. / Hirotsu, K. / Conway, M. / Yennawar, N. / Islam, M.M. / Hutson, S.M.
History
DepositionJun 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: branched chain aminotransferase
B: branched chain aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6337
Polymers82,7362
Non-polymers8975
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-32 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.823, 109.369, 59.252
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein branched chain aminotransferase


Mass: 41368.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: mitochondrial BCAT / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O15382, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GBN / [1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID / GABAPENTIN


Mass: 171.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO2 / Comment: medication*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 223 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.071 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002 / Details: mirrors
RadiationMonochromator: double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 68210 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.055 / Χ2: 1.031
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 100 % / Rmerge(I) obs: 0.347 / Num. measured obs: 3379 / Num. unique all: 3379 / Χ2: 1.116

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Phasing

Phasing MRRfactor: 39.5 / Cor.coef. Fo:Fc: 54 / Cor.coef. Io to Ic: 42
Highest resolutionLowest resolution
Rotation3.5 Å25.722 Å
Translation3.5 Å25.722 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.601data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3435 5 %RANDOM
Rwork0.208 ---
all0.208 ---
obs0.208 68169 99.1 %-
Solvent computationBsol: 21.468 Å2
Displacement parametersBiso mean: 24.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.875 Å20 Å2-0.701 Å2
2---0.56 Å20 Å2
3----0.315 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 58 341 6189
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3acy+glyc.par
X-RAY DIFFRACTION4gabapentin.par

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