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- PDB-4a0g: Structure of bifunctional DAPA aminotransferase-DTB synthetase fr... -

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Basic information

Entry
Database: PDB / ID: 4a0g
TitleStructure of bifunctional DAPA aminotransferase-DTB 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 / MOLECULAR REPLACEMENT / Resolution: 2.502 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
C: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
D: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,70720
Polymers365,7094
Non-polymers1,99816
Water7,728429
1
A: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,85310
Polymers182,8542
Non-polymers9998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-201.9 kcal/mol
Surface area50150 Å2
MethodPISA
2
C: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
D: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,85310
Polymers182,8542
Non-polymers9998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-176.9 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.442, 80.066, 136.939
Angle α, β, γ (deg.)99.96, 107.12, 97.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:43 OR RESSEQ 47:103 OR RESSEQ...
211(CHAIN B AND (RESSEQ 7:43 OR RESSEQ 47:1 OR RESSEQ...
112(CHAIN C AND (RESSEQ 7:43 OR RESSEQ 47:10 OR RESSEQ...
212((CHAIN D AND (RESSEQ 7:43 OR RESSEQ 47:1 RESSEQ 118:121...

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.999905, 0.011708, -0.007299), (0.004885, -0.194347, -0.980921), (-0.012904, -0.980863, 0.194271)-31.653, -21.332, -17.651
2given(-0.981547, -0.124762, 0.144911), (-0.105922, -0.276198, -0.955246), (0.159202, -0.952969, 0.257886)-12.402, -99.489, -73.988

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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.: 4 / 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) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: B0F481
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.15 Å3/Da / Density % sol: 42.8 % / Description: NONE
Crystal growDetails: BISTRIS 0.1 M PH 5.9, 0.2 M LISO4, 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 / Date: Oct 30, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979701 Å / Relative weight: 1
ReflectionResolution: 2.5→48.14 Å / Num. obs: 95045 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 1.95 % / Biso Wilson estimate: 40.31 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.81
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.91 / % possible all: 48.3

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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: 2.502→39.574 Å / SU ML: 0.88 / σ(F): 0 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 4750 5 %
Rwork0.1772 --
obs0.1803 94991 88.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.71 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.9288 Å21.8963 Å21.7088 Å2
2--0.9274 Å24.38 Å2
3---0.0014 Å2
Refinement stepCycle: LAST / Resolution: 2.502→39.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22123 0 112 429 22664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122912
X-RAY DIFFRACTIONf_angle_d1.32531237
X-RAY DIFFRACTIONf_dihedral_angle_d15.5248122
X-RAY DIFFRACTIONf_chiral_restr0.0833611
X-RAY DIFFRACTIONf_plane_restr0.0063966
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
21CX-RAY DIFFRACTIONPOSITIONAL
22DX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5017-2.53020.315870.26051638X-RAY DIFFRACTION49
2.5302-2.55990.3555960.25841834X-RAY DIFFRACTION53
2.5599-2.59110.31171040.24851983X-RAY DIFFRACTION58
2.5911-2.62390.34841120.24952114X-RAY DIFFRACTION62
2.6239-2.65850.32651260.24852402X-RAY DIFFRACTION70
2.6585-2.69490.34971380.25852616X-RAY DIFFRACTION77
2.6949-2.73340.33541600.25873048X-RAY DIFFRACTION89
2.7334-2.77410.34741720.24753257X-RAY DIFFRACTION95
2.7741-2.81750.36071710.23693247X-RAY DIFFRACTION95
2.8175-2.86370.3071730.22573305X-RAY DIFFRACTION96
2.8637-2.9130.34241710.22543230X-RAY DIFFRACTION96
2.913-2.9660.30211710.21183254X-RAY DIFFRACTION95
2.966-3.0230.30941700.19683234X-RAY DIFFRACTION96
3.023-3.08470.25281730.18433279X-RAY DIFFRACTION96
3.0847-3.15170.25321720.18153267X-RAY DIFFRACTION96
3.1517-3.2250.27881720.18873268X-RAY DIFFRACTION96
3.225-3.30560.23581740.1853307X-RAY DIFFRACTION96
3.3056-3.3950.25021720.17393267X-RAY DIFFRACTION96
3.395-3.49480.23771720.17313284X-RAY DIFFRACTION96
3.4948-3.60750.23941740.18323295X-RAY DIFFRACTION96
3.6075-3.73640.2441710.16933244X-RAY DIFFRACTION97
3.7364-3.88590.23221730.15713294X-RAY DIFFRACTION96
3.8859-4.06250.20311740.14493312X-RAY DIFFRACTION97
4.0625-4.27650.19831730.14313274X-RAY DIFFRACTION96
4.2765-4.54410.19021720.13733276X-RAY DIFFRACTION96
4.5441-4.89430.18881730.13373286X-RAY DIFFRACTION96
4.8943-5.38580.18151710.15483247X-RAY DIFFRACTION95
5.3858-6.16260.22951710.18583262X-RAY DIFFRACTION95
6.1626-7.75460.24621680.18063188X-RAY DIFFRACTION94
7.7546-39.57860.16031440.15542729X-RAY DIFFRACTION80
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)
12.473-0.61120.38252.26020.01532.4314-0.010.2679-0.0305-0.34850.08420.23810.0595-0.2539-0.02560.3271-0.0094-0.0640.36150.06260.2649-37.77989.8351-50.9761
21.3913-0.28820.24132.0698-0.01512.1947-0.02550.00990.1467-0.0603-0.02040.3161-0.3695-0.38630.06910.28420.0661-0.02360.36180.03140.3306-42.950121.1914-41.3472
30.7306-0.02470.25860.5398-0.07611.04420.00520.093-0.0975-0.0718-0.00030.0664-0.0167-0.1124-0.01530.17210.02520.01240.1795-0.03040.2343-23.41691.2478-28.969
41.3602-0.5911-0.4532.00360.03011.2158-0.071-0.2316-0.1920.39710.02060.30390.1892-0.03630.05080.2965-0.05740.03630.29780.01770.2303-30.6818-6.738812.2624
52.1493-0.13340.44580.76630.06771.30160.0227-0.15090.03790.1605-0.00180.1304-0.1-0.1385-0.02070.20890.00030.04280.14910.00190.1816-30.36352.0852-2.4445
62.61-0.0119-0.32082.8338-0.17022.141-0.03580.4410.1265-0.5798-0.0837-0.7648-0.03920.3210.09690.3479-0.05930.14040.37850.0880.47068.780123.718-40.5429
72.06640.21780.41092.9177-0.78081.34520.00390.2687-0.0054-0.3929-0.0355-0.4341-0.03640.18820.01360.223-0.00670.08350.2401-0.00850.2014-4.289119.4682-36.7739
80.9333-0.21590.05821.0905-0.07040.49770.037-0.0379-0.12550.0357-0.0173-0.11410.09810.0958-0.01260.17210.0077-0.01550.2003-0.02160.1852-3.8268-16.4834-16.7535
91.18680.1516-0.04531.84840.38821.9510.0045-0.09020.0070.00270.07940.23960.1368-0.2457-0.07790.2635-0.0785-0.01220.36690.08420.2943-33.1968-35.7493-58.9988
101.08850.0352-0.35420.9277-0.31431.70960.07650.07010.2284-0.15340.04630.13810.0582-0.2052-0.10660.2598-0.0105-0.02280.21420.01820.319-19.2555-20.1595-71.6949
111.5108-0.5361-0.10110.96190.05682.37930.39670.8490.1755-0.7866-0.14880.17060.0313-0.3991-0.18310.85720.1194-0.06240.78870.14810.367-16.1646-18.692-109.1286
122.40610.1379-0.0010.8736-0.31111.75090.1181.188-0.0472-0.5204-0.1220.52860.2457-1.12260.02130.7324-0.115-0.28451.11850.1050.6229-36.2839-26.604-98.5581
132.0002-0.29150.21942.67280.14311.8798-0.3166-0.35430.21820.7640.3614-0.68370.19760.4884-0.01590.43030.2047-0.18950.5689-0.11190.511116.4554-33.0984-61.3928
141.1145-0.4933-0.2612.4241-0.51350.7995-0.0265-0.06420.16580.01150.084-0.3250.07970.1474-0.04770.27680.0082-0.01370.2682-0.07040.23651.3413-24.172-73.998
151.82370.70340.15531.7993-0.09151.3069-0.03580.3922-0.0039-0.50210.21190.1456-0.06930.0899-0.16070.51280.02330.01170.3658-0.01970.3421-10.09714.0742-92.432
161.369-0.50110.58092.46690.0371.00740.0322-0.0296-0.0193-0.09810.0936-0.0494-0.09830.0347-0.11790.3512-0.00220.09930.30590.02150.2778-2.0279.997-82.5948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:92)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 93:171)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 172:450)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 451:580)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 581:811)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 5:143)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 144:289)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 290:811)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 6:171)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 172:430)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 431:709)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 710:806)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 7:143)
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 144:414)
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 415:529)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 530:807)

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