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- PDB-1bs0: PLP-DEPENDENT ACYL-COA SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1bs0
TitlePLP-DEPENDENT ACYL-COA SYNTHASE
ComponentsPROTEIN (8-AMINO-7-OXONANOATE SYNTHASE)
KeywordsTRANSFERASE / PLP-DEPENDENT ACYL-COA SYNTHASE / BIOTIN BIOSYNTHESIS / 8-AMINO-7-OXONANOATE SYNTHASE / 8-AMINO-7-KETOPELARGONATE SYNTHASE
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.65 Å
AuthorsAlexeev, D. / Alexeeva, M. / Baxter, R.L. / Campopiano, D.J. / Webster, S.P. / Sawyer, L.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme.
Authors: Alexeev, D. / Alexeeva, M. / Baxter, R.L. / Campopiano, D.J. / Webster, S.P. / Sawyer, L.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (8-AMINO-7-OXONANOATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9294
Polymers41,6411
Non-polymers2883
Water10,467581
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (8-AMINO-7-OXONANOATE SYNTHASE)
hetero molecules

A: PROTEIN (8-AMINO-7-OXONANOATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8598
Polymers83,2822
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area9750 Å2
ΔGint-156 kcal/mol
Surface area27440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.520, 58.520, 194.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-1330-

HOH

21A-1421-

HOH

31A-1527-

HOH

41A-1544-

HOH

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Components

#1: Protein PROTEIN (8-AMINO-7-OXONANOATE SYNTHASE) / E.C.2.3.1.47 TRANSFERASE / AONS / 8-AMINO-7-KETOPELARGONATE SYNTHASE


Mass: 41641.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B834(DE3) / Gene: BIOF / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P12998, 8-amino-7-oxononanoate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.31 Å3/Da / Density % sol: 46.3 %
Crystal growpH: 7.9
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS,, pH 7.9
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
3200 mMBis-Tris-propane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.911
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1996 / Details: BENT MIRROR
RadiationMonochromator: SUPPER DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 1.64→15 Å / Num. obs: 46252 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 31.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.369 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
MLPHAREphasing
DMmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.65→10 Å / Num. parameters: 14121 / Num. restraintsaints: 12231 / Cross valid method: R-FREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: SOME FURTHER REFINEMENT HAS BEEN PERFORMED SINCE THE PAPER WAS SUBMITTED TO J.MOL.BIOL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1390 3 %RANDOM
all0.1783 44628 --
obs0.1779 -99.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973) 201-228
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3359.1
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 15 581 3515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.002
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.092
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps0.08
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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