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- PDB-1iyd: CRYSTAL STRUCTURE OF ESCHELICHIA COLI BRANCHED-CHAIN AMINO ACID A... -

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Basic information

Entry
Database: PDB / ID: 1iyd
TitleCRYSTAL STRUCTURE OF ESCHELICHIA COLI BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
ComponentsBRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / HEXAMER / PLP
Function / homology
Function and homology information


aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / L-valine biosynthetic process / isoleucine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
Branched-chain amino acid aminotransferase I / 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 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV ...Branched-chain amino acid aminotransferase I / 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 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / 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
GLUTARIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHirotsu, K. / Goto, M.
CitationJournal: Biochemistry / Year: 2003
Title: Crystal structures of branched-chain amino Acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme.
Authors: Goto, M. / Miyahara, I. / Hayashi, H. / Kagamiyama, H. / Hirotsu, K.
History
DepositionAug 7, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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

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Assembly

Deposited unit
A: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
B: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
C: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5339
Polymers102,3953
Non-polymers1,1386
Water5,603311
1
A: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
B: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
C: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
hetero molecules

A: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
B: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
C: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,06518
Polymers204,7906
Non-polymers2,27612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area30110 Å2
ΔGint-96 kcal/mol
Surface area54130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.27, 99.02, 138.63
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE


Mass: 34131.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pUC119 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AB80, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GUA / GLUTARIC ACID


Mass: 132.115 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, HEPES, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
140 mg/mlprotein1drop
242 %(v/v)PEG4001drop
3200 mM1dropMgCl2
450 mMglutamate1drop
5100 mMsodium HEPES1droppH7.5
650 %(v/v)PEG4001reservoir
7100 mMglutarate1reservoir
850 mMglutamate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→19.96 Å / Num. all: 58165 / Num. obs: 58165 / % possible obs: 99.5 %
Reflection shellResolution: 2.15→2.22 Å / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 324820 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.195

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.242 5763
Rwork0.205 -
all-58165
obs-56634
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7086 0 72 311 7469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
Refinement
*PLUS
Lowest resolution: 19.96 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.22 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.259

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