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- PDB-4a0h: Structure of bifunctional DAPA aminotransferase-DTB synthetase fr... -

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Basic information

Entry
Database: PDB / ID: 4a0h
TitleStructure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to 7-keto 8-amino pelargonic acid (KAPA)
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
7-KETO-8-AMINOPELARGONIC ACID / PYRIDOXAL-5'-PHOSPHATE / L(+)-TARTARIC ACID / Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.808 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
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,39810
Polymers182,8542
Non-polymers1,5438
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-99.8 kcal/mol
Surface area46660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.320, 76.940, 89.220
Angle α, β, γ (deg.)90.00, 109.89, 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 7:41 OR RESSEQ 48:103 OR RESSEQ...
211(CHAIN B AND (RESSEQ 7:41 OR RESSEQ 48:103 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.695211, -0.09778, -0.712124), (-0.096469, -0.994434, 0.042365), (-0.712303, 0.039245, -0.700774)
Vector: 18.62476, -31.90849, 48.69297)

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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: 91427.188 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / 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-KAP / 7-KETO-8-AMINOPELARGONIC ACID


Mass: 187.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO3
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6

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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: 39.3 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM TARTRATE PH 6.2, 15 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979701
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979701 Å / Relative weight: 1
ReflectionResolution: 2.81→44.57 Å / Num. obs: 36581 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Biso Wilson estimate: 52.68 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.22
Reflection shellResolution: 2.81→2.88 Å / Redundancy: 1.74 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.61 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A0F

4a0f


Resolution: 2.808→44.572 Å / SU ML: 0.74 / σ(F): 1.99 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 1822 5 %
Rwork0.1934 --
obs0.197 36557 99.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.332 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 66.7 Å2
Baniso -1Baniso -2Baniso -3
1--11.072 Å20 Å25.2037 Å2
2--19.4404 Å20 Å2
3----8.3684 Å2
Refinement stepCycle: LAST / Resolution: 2.808→44.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11346 0 102 0 11448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111719
X-RAY DIFFRACTIONf_angle_d1.35415937
X-RAY DIFFRACTIONf_dihedral_angle_d16.3454185
X-RAY DIFFRACTIONf_chiral_restr0.081832
X-RAY DIFFRACTIONf_plane_restr0.0062027
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 (%)
2.8082-2.88410.36551340.2892472X-RAY DIFFRACTION92
2.8841-2.96890.33391190.25542681X-RAY DIFFRACTION100
2.9689-3.06480.35041440.24992652X-RAY DIFFRACTION100
3.0648-3.17430.32311270.23392717X-RAY DIFFRACTION100
3.1743-3.30130.33841400.22992651X-RAY DIFFRACTION100
3.3013-3.45150.35771230.21742687X-RAY DIFFRACTION100
3.4515-3.63340.28321690.20642658X-RAY DIFFRACTION100
3.6334-3.86090.27841470.17052690X-RAY DIFFRACTION100
3.8609-4.15880.21841410.16622658X-RAY DIFFRACTION100
4.1588-4.5770.20641410.13872711X-RAY DIFFRACTION100
4.577-5.23840.18931570.14772693X-RAY DIFFRACTION100
5.2384-6.59640.27591480.2082703X-RAY DIFFRACTION100
6.5964-44.57760.22821320.19412762X-RAY DIFFRACTION98
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)
10.68390.09220.20190.6723-0.06081.1082-0.24170.1899-0.553-0.04990.18560.01070.2148-0.2729-0.00480.4222-0.1440.13380.4237-0.13510.6696-7.7929-40.111128.6287
20.7562-0.0386-0.02260.3260.01790.6208-0.06730.2072-0.1931-0.08520.0016-0.02050.0699-0.02670.04220.3397-0.06220.01490.334-0.040.306220.097-26.242120.0755
30.9694-0.27170.09960.55290.0140.627-0.11070.0337-0.14390.04850.0283-0.0650.12170.17610.06560.35570.00790.02120.41870.00190.467643.0012-29.342728.8837
40.5523-0.11750.17690.7085-0.00990.9597-0.11830.11820.3053-0.16220.0990.0462-0.18970.08030.02640.40290.0192-0.07080.2531-0.05580.5176-2.43848.940830.8941
50.738-0.12260.01190.45730.08270.6521-0.05710.42440.1817-0.21410.0197-0.137-0.17580.11060.02670.4254-0.10490.00520.47950.0540.328826.1347-7.20089.554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:143)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 144:520)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 521:807)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 7:170)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 171:807)

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