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- PDB-1i1m: CRYSTAL STRUCTURE OF ESCHERICHIA COLI BRANCHED-CHAIN AMINO ACID A... -

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Basic information

Entry
Database: PDB / ID: 1i1m
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE.
ComponentsBRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / HEXAMER / PLP / 4-METHYLVARELATE
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
4-METHYL VALERIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOkada, K. / Hirotsu, K. / Hayashi, H. / Kagamiyama, H.
CitationJournal: Biochemistry / Year: 2001
Title: Structures of Escherichia coli branched-chain amino acid aminotransferase and its complexes with 4-methylvalerate and 2-methylleucine: induced fit and substrate recognition of the enzyme.
Authors: Okada, K. / Hirotsu, K. / Hayashi, H. / Kagamiyama, H.
History
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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

Downloads & links

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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)103,4859
Polymers102,3953
Non-polymers1,0906
Water5,314295
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)206,96918
Polymers204,7906
Non-polymers2,18012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area28250 Å2
ΔGint-133 kcal/mol
Surface area56110 Å2
MethodPISA
2
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)206,96918
Polymers204,7906
Non-polymers2,18012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)155.990, 100.710, 141.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / 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-4MV / 4-METHYL VALERIC ACID


Mass: 116.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlprotein1drop
20.1 MHEPES1drop
30.010 mMPLP1drop
41 mMsodium azide1drop
528 %(w/v)PEG4001reservoir
60.1 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 21, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 42569 / % possible obs: 98.9 % / Num. measured all: 134092 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.165

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber /
RfactorSelection details
Rfree0.215 RANDOM
Rwork0.173 -
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7086 0 69 295 7450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / σ(F): 0 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.2
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / Rfactor Rfree: 0.276 / Rfactor obs: 0.234

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