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- PDB-1qj5: Crystal structure of 7,8-diaminopelargonic acid synthase -

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Basic information

Entry
Database: PDB / ID: 1qj5
TitleCrystal structure of 7,8-diaminopelargonic acid synthase
Components7,8-DIAMINOPELARGONIC ACID SYNTHASE
KeywordsAMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / BIOTIN BIOSYNTHESIS
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
: / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKack, H. / Sandmark, J. / Gibson, K.J. / Lindqvist, Y. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships between Pyridoxal-5'-Phosphate Dependent Enzymes
Authors: Kack, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y.
History
DepositionJun 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-DIAMINOPELARGONIC ACID SYNTHASE
B: 7,8-DIAMINOPELARGONIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1936
Polymers94,6212
Non-polymers5724
Water10,016556
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-94.9 kcal/mol
Surface area33460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.338, 55.556, 120.884
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99995, 0.01019, 0.0007), (0.01019, 0.99051, 0.13706), (0.0007, 0.13706, -0.99056)
Vector: -48.6763, -11.998, 177.85899)
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein 7,8-DIAMINOPELARGONIC ACID SYNTHASE


Mass: 47310.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Cellular location: CYTOPLASM / Gene: BIOA / Plasmid: PET24 / Cellular location (production host): CYTOPLASM / Gene (production host): BIOA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTRP14 IS OBSERVED AS A LEU RESIDUE.

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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: 2.2 Å3/Da / Density % sol: 30 %
Crystal growpH: 6.7 / Details: pH 6.70
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
221 %PEG40001reservoirprecipitant
312 %2-propanol1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8265, 0.9082, 0.9918, 1.007
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.82651
20.90821
30.99181
41.0071
ReflectionResolution: 1.8→20 Å / Num. obs: 149599 / % possible obs: 94.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.305 / % possible all: 81.3
Reflection
*PLUS
Num. obs: 67496 / Num. measured all: 149599 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.305

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: BREAK IN CHAIN A, RESIDUE ASP 183 IS MISSING DUE TO DISORDER. ONLY MAIN-CHAIN ATOMS AND THE CB ATOM IS INCLUDED FOR GLU185 CHAIN B, DUE TO DISORDER. ONLY BACKBONE OF C-TERMINAL RESIDUE WAS ...Details: BREAK IN CHAIN A, RESIDUE ASP 183 IS MISSING DUE TO DISORDER. ONLY MAIN-CHAIN ATOMS AND THE CB ATOM IS INCLUDED FOR GLU185 CHAIN B, DUE TO DISORDER. ONLY BACKBONE OF C-TERMINAL RESIDUE WAS SEEN IN ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 -5 %RANDOM
Rwork0.175 ---
obs-67496 94.4 %-
Displacement parametersBiso mean: 21.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 32 556 7196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8383
X-RAY DIFFRACTIONp_mcangle_it2.4075
X-RAY DIFFRACTIONp_scbond_it4.1646
X-RAY DIFFRACTIONp_scangle_it5.2948
X-RAY DIFFRACTIONp_plane_restr0.0203
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor16.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor15

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