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- PDB-1s0a: Crystal Structure of the Y17F Mutant of 7,8-Diaminopelargonic Aci... -

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Basic information

Entry
Database: PDB / ID: 1s0a
TitleCrystal Structure of the Y17F 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 / MOLECULAR REPLACEMENT / Resolution: 1.71 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 / 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_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

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)95,0914
Polymers95,0452
Non-polymers462
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-108 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.508, 55.659, 121.396
Angle α, β, γ (deg.)90.00, 97.04, 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: 47522.508 Da / Num. of mol.: 2 / Mutation: Y17F
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.: 660 / 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: 40.37 %
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: 1.13 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: 1.71→20 Å / Num. all: 83943 / Num. obs: 81593 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.096 / Net I/σ(I): 11.5
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.408 / % possible all: 90.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 81351 / Num. measured all: 325020 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 90.7 % / Rmerge(I) obs: 0.408

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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: 1.71→19.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.686 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20557 4065 5 %RANDOM
Rwork0.18592 ---
all0.19 77492 --
obs0.18692 77492 98.77 %-
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: 21.231 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20.44 Å2
2--1.74 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.71→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 2 660 7358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216759
X-RAY DIFFRACTIONr_bond_other_d0.0010.026172
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9459188
X-RAY DIFFRACTIONr_angle_other_deg1.155314279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6873852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39151162
X-RAY DIFFRACTIONr_chiral_restr0.090.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027556
X-RAY DIFFRACTIONr_gen_planes_other0.010.021372
X-RAY DIFFRACTIONr_nbd_refined0.2620.31538
X-RAY DIFFRACTIONr_nbd_other0.210.35920
X-RAY DIFFRACTIONr_nbtor_other0.3030.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5594
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0920.511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4020.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.510.530
X-RAY DIFFRACTIONr_mcbond_it0.5091.54265
X-RAY DIFFRACTIONr_mcangle_it0.94426840
X-RAY DIFFRACTIONr_scbond_it1.41732494
X-RAY DIFFRACTIONr_scangle_it2.3074.52348
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 258
Rwork0.286 4966
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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