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- PDB-4a0f: Structure of selenomethionine substituted bifunctional DAPA amino... -

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Basic information

Entry
Database: PDB / ID: 4a0f
TitleStructure of selenomethionine substituted bifunctional DAPA aminotransferase-dethiobiotin synthetase from Arabidopsis thaliana in its apo form.
ComponentsADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
KeywordsTRANSFERASE / BIO3-BIO1 / BIOTIN SYNTHESIS
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / dethiobiotin synthase / dethiobiotin synthase activity / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / magnesium ion binding / protein homodimerization activity / mitochondrion / ATP binding
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Dethiobiotin synthase BioD / AAA domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.714 Å
AuthorsCobessi, D. / Dumas, R. / Pautre, V. / Meinguet, C. / Ferrer, J.L. / Alban, C.
CitationJournal: Plant Cell / Year: 2012
Title: Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis.
Authors: Cobessi, D. / Dumas, R. / Pautre, V. / Meinguet, C. / Ferrer, J.L. / Alban, C.
History
DepositionSep 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,2668
Polymers184,3872
Non-polymers8796
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-168.2 kcal/mol
Surface area48440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.670, 75.970, 88.630
Angle α, β, γ (deg.)90.00, 109.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 6:41 OR RESSEQ 48:10 OR RESSEQ...
211(CHAIN B AND (RESSEQ 6:41 OR RESSEQ 48:103 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.691954, 0.064938, -0.719015), (0.072401, -0.997167, -0.020384), (-0.718302, -0.037952, -0.694696)
Vector: 39.65007, 39.98365, 97.19749)

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Components

#1: Protein ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE / DTB SYNTHETASE-DAPA AMINOTRANSFERASE / MITOCHONDRIAL BIFUNCTIONAL DIAMINOPELARGONATE SYNTHASE- ...DTB SYNTHETASE-DAPA AMINOTRANSFERASE / MITOCHONDRIAL BIFUNCTIONAL DIAMINOPELARGONATE SYNTHASE-DETHIOBIOTIN SYNTHETASE / ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE/DETHIOBIOTIN SYNTHETASE


Mass: 92193.523 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-833 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: B0F481
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 348 TO TYR ENGINEERED RESIDUE IN CHAIN B, PHE 348 TO TYR

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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 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growDetails: BISTRIS 0.1 M PH 5.9, 0.2 M LISO4, 15 % PEG3350, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 2.72→40.33 Å / Num. obs: 76488 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 47.96 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.88
Reflection shellResolution: 2.71→2.78 Å / Redundancy: 2.93 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.11 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.714→41.849 Å / SU ML: 0.8 / σ(F): 1.99 / Phase error: 27.85 / Stereochemistry target values: ML / Details: FRIEDEL'S MATES HAVE BEEN MERGED.
RfactorNum. reflection% reflection
Rfree0.261 1989 5 %
Rwork0.1996 --
obs0.2027 39553 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.039 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1--11.268 Å20 Å2-3.5913 Å2
2--1.272 Å20 Å2
3---9.9959 Å2
Refinement stepCycle: LAST / Resolution: 2.714→41.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11182 0 50 80 11312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911490
X-RAY DIFFRACTIONf_angle_d1.23615674
X-RAY DIFFRACTIONf_dihedral_angle_d14.4023990
X-RAY DIFFRACTIONf_chiral_restr0.0761822
X-RAY DIFFRACTIONf_plane_restr0.0051996
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7144-2.78220.3491330.2432453X-RAY DIFFRACTION92
2.7822-2.85750.30071330.23182679X-RAY DIFFRACTION100
2.8575-2.94150.32041270.2262690X-RAY DIFFRACTION100
2.9415-3.03640.3161450.21982709X-RAY DIFFRACTION100
3.0364-3.14490.29611350.20812705X-RAY DIFFRACTION100
3.1449-3.27080.31251470.21172676X-RAY DIFFRACTION100
3.2708-3.41960.26881730.20542663X-RAY DIFFRACTION100
3.4196-3.59980.30711500.22722665X-RAY DIFFRACTION99
3.5998-3.82520.29671350.2192710X-RAY DIFFRACTION99
3.8252-4.12030.26651270.1932645X-RAY DIFFRACTION98
4.1203-4.53450.20271420.15362741X-RAY DIFFRACTION100
4.5345-5.18960.20381340.15822723X-RAY DIFFRACTION100
5.1896-6.53430.25871430.20042734X-RAY DIFFRACTION100
6.5343-41.85420.21931650.20622771X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.26030.5661-0.16932.90680.43173.34180.1218-0.075-0.2461-0.1530.09460.1919-0.2403-0.0413-0.1870.331-0.04690.02370.2367-0.00530.312299.467844.23936.9373
21.77880.7035-0.2561.5739-0.64541.39260.0597-0.14390.2410.1523-0.0199-0.1833-0.1773-0.0216-0.03780.28720.0073-0.02710.2806-0.02710.3595102.90840.24919.2643
33.05350.881-0.78610.35780.40390.67220.13650.12920.7775-0.1322-0.07890.2668-0.3258-0.222-0.04170.43860.0713-0.11280.32650.00850.534475.828941.839112.9448
42.04830.67480.03262.1708-0.35370.8680.1673-0.72080.37310.6668-0.20440.3499-0.2238-0.08110.01920.5345-0.06630.06890.5865-0.12420.320670.077830.56642.5058
52.16930.85990.05191.17380.28342.98210.0048-0.044-0.8165-0.0366-0.0005-0.51550.40540.2550.04480.4370.0840.02870.326-0.00390.9521107.1322-1.134313.7032
62.35790.3634-0.11221.099-0.03850.67250.0602-0.0559-0.3650.1743-0.09040.05490.1566-0.1330.0260.3608-0.019-0.00640.2899-0.04460.234973.869113.169321.4003
72.39520.05420.47292.56370.45451.24410.00850.3389-0.4226-0.00160.04850.07910.26790.0107-0.03710.265-0.02340.02190.4173-0.10920.343964.39219.035214.5192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 6:65)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 66:289)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 290:363)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 364:808)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 5:188)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 189:607)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 608:808)

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