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- PDB-2hgw: Crystal structure of Cys318Ala mutant of human mitochondrial bran... -

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Basic information

Entry
Database: PDB / ID: 2hgw
TitleCrystal structure of Cys318Ala mutant of human mitochondrial branched chain aminotransferase
ComponentsBranched-chain-amino-acid aminotransferase, mitochondrial
KeywordsTRANSFERASE / D-aminoacid aminotransferase-like PLP-dependent enzymes
Function / homology
Function and homology information


regulation of hormone levels / branched-chain-amino-acid transaminase activity / 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 catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / 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 catabolism / L-leucine biosynthetic process / valine 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 / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYennawar, N.H. / Hutson, S.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Human Mitochondrial Branched Chain Aminotransferase Isozyme: STRUCTURAL ROLE OF THE CXXC CENTER IN CATALYSIS.
Authors: Yennawar, N.H. / Islam, M.M. / Conway, M. / Wallin, R. / Hutson, S.M.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Branched-chain-amino-acid aminotransferase, mitochondrial
B: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,19317
Polymers82,6722
Non-polymers1,52115
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-51 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.668, 105.585, 106.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCATm / Placental protein 18 / PP18 / Mitochondrial Branched Chain Aminotransferase


Mass: 41335.953 Da / Num. of mol.: 2 / Mutation: C318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, ECA40 / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21de3
References: UniProt: O15382, branched-chain-amino-acid transaminase

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Non-polymers , 6 types, 187 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG1500, DTT, HEPES pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91609 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91609 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. all: 55534 / Num. obs: 54317 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 / Χ2: 1.116 / Net I/σ(I): 7.8
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 0.822 / Num. unique all: 2632 / Χ2: 1.083 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→25 Å / FOM work R set: 0.827 / σ(F): 1208 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2624 4.7 %RANDOM
Rwork0.227 ---
obs0.227 53020 95.6 %-
all-55534 --
Solvent computationBsol: 28.065 Å2
Displacement parametersBiso mean: 33.223 Å2
Baniso -1Baniso -2Baniso -3
1-12.36 Å20 Å20 Å2
2---12.721 Å20 Å2
3---0.361 Å2
Refinement stepCycle: LAST / Resolution: 1.98→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 96 172 5983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.98-1.990.269420.306932974
1.99-2.010.328590.329641023
2.01-2.020.28500.3159741024
2.02-2.040.343590.2939501009
2.04-2.050.289410.296950991
2.05-2.070.3510.2889671018
2.07-2.080.354660.289701036
2.08-2.10.279580.2929431001
2.1-2.120.274520.2819751027
2.12-2.130.28500.2569681018
2.13-2.150.333500.2819831033
2.15-2.170.244520.2699641016
2.17-2.190.25480.2699841032
2.19-2.210.302690.2669531022
2.21-2.230.305410.2589931034
2.23-2.250.315560.2599691025
2.25-2.270.255470.2579911038
2.27-2.30.295450.23610081053
2.3-2.320.248500.2419731023
2.32-2.350.333540.2529771031
2.35-2.370.245630.2239721035
2.37-2.40.27630.2499861049
2.4-2.430.255560.2459911047
2.43-2.460.347500.24110031053
2.46-2.490.29430.23510211064
2.49-2.530.266390.2310101049
2.53-2.560.222420.2149951037
2.56-2.60.255540.23810231077
2.6-2.640.306560.23710001056
2.64-2.690.291500.21410341084
2.69-2.730.275640.21610081072
2.73-2.780.271650.22510211086
2.78-2.840.248490.21710261075
2.84-2.890.257540.21610601114
2.89-2.960.239590.22310221081
2.96-3.030.278500.20710411091
3.03-3.10.257480.21710401088
3.1-3.180.207580.20310331091
3.18-3.280.271470.20310291076
3.28-3.380.243510.21610531104
3.38-3.50.223580.19710401098
3.5-3.640.213520.18510601112
3.64-3.810.246480.19510521100
3.81-4.010.178450.19610391084
4.01-4.260.229420.21810491091
4.26-4.590.234570.22110251082
4.59-5.040.25490.21110571106
5.04-5.770.273480.2510821130
5.77-7.240.267630.25810911154
7.24-250.216610.20411451206
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3acy+glyc.par

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