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- PDB-3dod: Crystal Structure of PLP Bound 7,8-Diaminopelargonic Acid Synthas... -

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Basic information

Entry
Database: PDB / ID: 3dod
TitleCrystal Structure of PLP Bound 7,8-Diaminopelargonic Acid Synthase in Bacillus subtilis
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / BIOTIN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE / S-adenosyl-L-methionine
Function / homology
Function and homology information


lysine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / 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 ...Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-Lysine--8-amino-7-oxononanoate transaminase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDey, S. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 2010
Title: Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
Authors: Dey, S. / Lane, J.M. / Lee, R.E. / Rubin, E.J. / Sacchettini, J.C.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8434
Polymers100,3492
Non-polymers4942
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-73 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.674, 104.027, 73.868
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / 7 / 8-diamino-pelargonic acid aminotransferase / DAPA aminotransferase


Mass: 50174.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: bioA, BSU30230 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53555, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2M sodium thiocyanate, 5% xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.9→58.8 Å / Num. obs: 65688 / % possible obs: 99.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3bv0

3bv0


Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.031 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24022 3330 5.1 %RANDOM
Rwork0.19571 ---
obs0.19794 62200 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.155 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20.56 Å2
2--1.11 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 30 384 6966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226741
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9799094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.865296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1526
X-RAY DIFFRACTIONr_chiral_restr0.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.025005
X-RAY DIFFRACTIONr_nbd_refined0.33521
X-RAY DIFFRACTIONr_nbtor_refined0.54619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.5796
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.514
X-RAY DIFFRACTIONr_mcbond_it54238
X-RAY DIFFRACTIONr_mcangle_it76653
X-RAY DIFFRACTIONr_scbond_it92803
X-RAY DIFFRACTIONr_scangle_it112441
LS refinement shellResolution: 1.9→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 233 -
Rwork0.274 4290 -
obs--92.06 %

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