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- PDB-1mgv: Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Ac... -

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Basic information

Entry
Database: PDB / ID: 1mgv
TitleCrystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase
Components7,8-diamino-pelargonic acid aminotransferase
KeywordsTRANSFERASE / Aminotransferase / fold type I / subclass II / homodimer
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / 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
ISOPROPYL ALCOHOL / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEliot, A.C. / Sandmark, J. / Schneider, G. / Kirsch, J.F.
CitationJournal: Biochemistry / Year: 2002
Title: The Dual-Specific Active Site of 7,8-Diaminopelargonic Acid Synthase and the Effect of the R391A Mutation
Authors: Eliot, A.C. / Sandmark, J. / Schneider, G. / Kirsch, J.F.
History
DepositionAug 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999sequence the authors maintain that residue 14 is a leucine, as confirmed by DNA sequencing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-diamino-pelargonic acid aminotransferase
B: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,22910
Polymers94,4492
Non-polymers7818
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-89 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.880, 55.899, 116.237
Angle α, β, γ (deg.)90.00, 110.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-869-

HOH

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Components

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


Mass: 47224.273 Da / Num. of mol.: 2 / Mutation: R391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bioA / Plasmid: pet24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, MPD, HEPES, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion / Details: Kack, H., (1998) Acta Crystallogr., D54, 1397.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
221 %PEG40001reservoirpH7.3
312 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.12 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2001
RadiationMonochromator: Si(111) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.1→20.08 Å / Num. all: 44984 / Num. obs: 44984 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.21 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.168 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 43771 / Num. measured all: 177643 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.168

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WT dimer

Resolution: 2.1→20.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.417 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2269 5 %RANDOM
Rwork0.2014 ---
all0.2031 42715 --
obs0.2031 42715 --
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: 32.259 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.09 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 48 342 6974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216794
X-RAY DIFFRACTIONr_bond_other_d0.0010.026169
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9479234
X-RAY DIFFRACTIONr_angle_other_deg1.225314310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0113855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.966151177
X-RAY DIFFRACTIONr_chiral_restr0.0820.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027582
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021359
X-RAY DIFFRACTIONr_nbd_refined0.2640.31798
X-RAY DIFFRACTIONr_nbd_other0.2230.36452
X-RAY DIFFRACTIONr_nbtor_other0.6110.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.5548
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.516
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7540.516
X-RAY DIFFRACTIONr_mcbond_it0.6861.54271
X-RAY DIFFRACTIONr_mcangle_it1.26926851
X-RAY DIFFRACTIONr_scbond_it1.72432523
X-RAY DIFFRACTIONr_scangle_it2.8484.52382
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 170
Rwork0.258 2986
Refinement
*PLUS
Rfactor Rfree: 0.233 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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