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- PDB-1s08: Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Ac... -

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Basic information

Entry
Database: PDB / ID: 1s08
TitleCrystal Structure of the D147N 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 / 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
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Mar 7, 2018Group: 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 1.4Oct 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 / 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 1.5Apr 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)95,1214
Polymers95,0752
Non-polymers462
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-93 kcal/mol
Surface area27590 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: 47537.523 Da / Num. of mol.: 2 / Mutation: D147N
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.: 402 / 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: 40.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
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: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2002
RadiationMonochromator: Si(111) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 48622 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.331 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 44599 / Num. measured all: 149282 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.331

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Processing

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

Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.139 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residue 133 is located in a flexible surface loop, which is not very well defined in the electron density. This gives rise to the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residue 133 is located in a flexible surface loop, which is not very well defined in the electron density. This gives rise to the deviations from the standard geometry.
RfactorNum. reflection% reflectionSelection details
Rfree0.22728 2621 5.1 %RANDOM
Rwork0.20161 ---
all0.2029 44599 --
obs0.20294 44599 96.72 %-
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: 28.356 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20.74 Å2
2--3.41 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 2 402 6840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216447
X-RAY DIFFRACTIONr_bond_other_d0.0020.025909
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9468749
X-RAY DIFFRACTIONr_angle_other_deg1.6313662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9093802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.243151108
X-RAY DIFFRACTIONr_chiral_restr0.1080.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027142
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021306
X-RAY DIFFRACTIONr_nbd_refined0.2610.31452
X-RAY DIFFRACTIONr_nbd_other0.2180.35599
X-RAY DIFFRACTIONr_nbtor_other0.180.513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.5447
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2120.59
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.325
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4630.59
X-RAY DIFFRACTIONr_mcbond_it0.6451.54053
X-RAY DIFFRACTIONr_mcangle_it1.19526492
X-RAY DIFFRACTIONr_scbond_it1.67732394
X-RAY DIFFRACTIONr_scangle_it2.7414.52257
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 194
Rwork0.248 2145
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.227 / 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_deg1.6

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