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- PDB-1wrv: Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotran... -

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Basic information

Entry
Database: PDB / ID: 1wrv
TitleCrystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase
ComponentsBranched-Chain Amino Acid Aminotransferase
KeywordsTRANSFERASE / hexamer / PLP-dependent enzyme / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / 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 ...Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / 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
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGoto, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase
Authors: Goto, M. / Miyahara, I. / Hirotsu, K.
History
DepositionOct 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)103,65814
Polymers102,2193
Non-polymers1,43911
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)207,31528
Polymers204,4386
Non-polymers2,87722
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area35670 Å2
ΔGint-336 kcal/mol
Surface area50070 Å2
MethodPISA
3
A: Branched-Chain Amino Acid Aminotransferase
hetero molecules

C: Branched-Chain Amino Acid Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0669
Polymers68,1462
Non-polymers9207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
4
C: Branched-Chain Amino Acid Aminotransferase
hetero molecules

A: Branched-Chain Amino Acid Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0669
Polymers68,1462
Non-polymers9207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
5
B: Branched-Chain Amino Acid Aminotransferase
hetero molecules

B: Branched-Chain Amino Acid Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,18410
Polymers68,1462
Non-polymers1,0388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)143.410, 143.410, 116.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Branched-Chain Amino Acid Aminotransferase / / IlvE


Mass: 34072.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5SM19, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: NaCl, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→19.96 Å / Num. all: 192751 / Num. obs: 171549 / % possible obs: 89 % / Biso Wilson estimate: 15.4 Å2
Reflection shellResolution: 1.5→1.58 Å / % possible all: 85.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→9.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3259499.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.218 16911 9.9 %RANDOM
Rwork0.205 ---
obs0.205 170262 88.8 %-
all-191362 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.1304 Å2 / ksol: 0.524713 e/Å3
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 88 312 7387
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.282
X-RAY DIFFRACTIONc_scbond_it9.842
X-RAY DIFFRACTIONc_scangle_it8.042.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 2684 10 %
Rwork0.248 24221 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCNS_LOCAL:TOP.WAT
X-RAY DIFFRACTION3CNS_LOCAL:PARAM.PLPCNS_LOCAL:TOP.PLP
X-RAY DIFFRACTION4CNS_LOCAL:PARAM.ETCINTSHIFF.TOP
X-RAY DIFFRACTION5MPD.PARAMMPD.TOP
X-RAY DIFFRACTION6ION.PARAMION.TOP

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