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- PDB-1dj9: CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AM... -

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Basic information

Entry
Database: PDB / ID: 1dj9
TitleCRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.
Components8-AMINO-7-OXONONANOATE SYNTHASE
KeywordsTRANSFERASE / 8-AMINO-7-OXONONANOATE SYNTHASE / BIOTIN / PYRIDOXAL-5'-PHOSPHATE
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
Chem-KAM / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 2 Å
AuthorsWebster, S.P. / Alexeev, D. / Campopiano, D.J. / Watt, R.M. / Alexeeva, M. / Sawyer, L. / Baxter, R.L.
Citation
Journal: Biochemistry / Year: 2000
Title: Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies.
Authors: Webster, S.P. / Alexeev, D. / Campopiano, D.J. / Watt, R.M. / Alexeeva, M. / Sawyer, L. / Baxter, R.L.
#1: Journal: 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. / WEBSTER, S.P. / SAWYER, L.
History
DepositionDec 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
A: 8-AMINO-7-OXONONANOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1745
Polymers41,5391
Non-polymers6354
Water6,071337
1


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

A: 8-AMINO-7-OXONONANOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,34810
Polymers83,0782
Non-polymers1,2708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area11620 Å2
ΔGint-141 kcal/mol
Surface area25520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.890, 58.890, 201.770
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-1190-

HOH

21A-1292-

HOH

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Components

#1: Protein 8-AMINO-7-OXONONANOATE SYNTHASE / 7-KAP SYNTHETASE


Mass: 41539.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P12998, 8-amino-7-oxononanoate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KAM / N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-7-KETO-8-AMINOPELARGONIC ACID-5'-MONOPHOSPHATE


Mass: 418.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMbis-Tris/propane1drop
350-100 mM1dropNaCl
41.6 Mammonium sulfate1reservoir
5200 mMbis-Tris/propane1reservoir
630 %(v/v)glycerol1reservoir
70.1 mMAON1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.99→31.62 Å / Num. all: 28007 / Num. obs: 27822 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 6.3
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.452 / % possible all: 93.5
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 2→10 Å / Num. parameters: 1320 / Num. restraintsaints: 1230 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.278 820 -RANDOM
Rwork0.212 ---
all0.212 27177 --
obs0.212 27314 99.5 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3208
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 39 337 3288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.1
X-RAY DIFFRACTIONs_approx_iso_adps0

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