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- PDB-1s06: Crystal Structure of the R253K Mutant of 7,8-Diaminopelargonic Ac... -

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Basic information

Entry
Database: PDB / ID: 1s06
TitleCrystal Structure of the R253K Mutant of 7,8-Diaminopelargonic Acid Synthase
ComponentsAdenosylmethionine-8-amino-7-oxononanoate 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 / 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
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsSandmark, J. / Eliot, A.C. / Famm, K. / Schneider, G. / Kirsch, J.F.
CitationJournal: Biochemistry / Year: 2004
Title: Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis.
Authors: Sandmark, J. / Eliot, A.C. / Famm, K. / Schneider, G. / Kirsch, J.F.
History
DepositionDec 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 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 / pdbx_unobs_or_zero_occ_residues / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999 The crystallised protein differs from the Swissprot sequence at residue 14. In the Swissprot ... The crystallised protein differs from the Swissprot sequence at residue 14. In the Swissprot sequence number 14 is a tryptophan while in this structure it is a leucin. This is confirmed by DNA sequencing and was also reported for the original wild-type structure (1qj5).

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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)95,0674
Polymers95,0212
Non-polymers462
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-106 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.080, 56.527, 120.993
Angle α, β, γ (deg.)90.00, 96.32, 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: 47510.492 Da / Num. of mol.: 2 / Mutation: R253K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BIOA, B0774 / Plasmid: pT7bioA / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126-28 %PEG40001reservoir
29-12 %MPD1reservoir
3100 mMHEPES1reservoirpH7.5
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.13 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 14, 2002
RadiationMonochromator: Si(111)monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 39945 / Num. obs: 39626 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.124 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.421 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. measured all: 138828 / Rmerge(I) obs: 0.124
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.421

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SFALLphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: WT dimer

Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.568 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22567 2010 5.1 %RANDOM
Rwork0.191 ---
all0.193 37212 --
obs0.19327 37212 98.21 %-
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: 25.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.6 Å2
2--3.3 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 2 336 7004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216788
X-RAY DIFFRACTIONr_bond_other_d0.0020.026189
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9469222
X-RAY DIFFRACTIONr_angle_other_deg1.183314340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8243851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25151184
X-RAY DIFFRACTIONr_chiral_restr0.0840.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027575
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021370
X-RAY DIFFRACTIONr_nbd_refined0.2680.31511
X-RAY DIFFRACTIONr_nbd_other0.2120.35885
X-RAY DIFFRACTIONr_nbtor_other0.2980.57
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5419
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.10.511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4160.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4680.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4970.57
X-RAY DIFFRACTIONr_symmetry_hbond_other0.5030.51
X-RAY DIFFRACTIONr_mcbond_it0.5731.54257
X-RAY DIFFRACTIONr_mcangle_it1.07526822
X-RAY DIFFRACTIONr_scbond_it1.73932531
X-RAY DIFFRACTIONr_scangle_it2.9554.52400
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 130
Rwork0.239 2357
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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