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Basic information

Entry
Database: PDB / ID: 1dbs
TitleMECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE
ComponentsDETHIOBIOTIN SYNTHETASE
KeywordsBIOTIN BIOSYNTHESIS
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
CobQ/CobB/MinD/ParA nucleotide binding domain / Dethiobiotin synthase BioD / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent dethiobiotin synthetase BioD 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSawyer, L. / Alexeev, D.
Citation
Journal: Structure / Year: 1994
Title: Mechanistic implications and family relationships from the structure of dethiobiotin synthetase.
Authors: Alexeev, D. / Baxter, R.L. / Sawyer, L.
#1: Journal: Structure / Year: 1994
Title: Crystal Structure of an ATP Dependent Carboxylase Dethiobiotin Synthetase at 1.65 Angstroms Resolution
Authors: Huang, W. / Lundquist, Y. / Schneider, G. / Gibson, K.J. / Flint, D. / Lorimer, G.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Sequence and Crystallization of Escherichia Coli Dethiobiotin Synthetase, the Penultimate Enzyme of Biotin Biosynthesis
Authors: Alexeev, D. / Baxter, R.L.
History
DepositionNov 29, 1994Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3164
Polymers24,0281
Non-polymers2883
Water3,621201
1
A: DETHIOBIOTIN SYNTHETASE
hetero molecules

A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6338
Polymers48,0572
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)72.874, 49.000, 61.309
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: LOOP 209 - 212 HAS POOR ELECTRON DENSITY. / 2: HOH 403 MAY BE A SODIUM ION.

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Components

#1: Protein DETHIOBIOTIN SYNTHETASE


Mass: 24028.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHOH 403 MAY BE A SODIUM ION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal
*PLUS
Density % sol: 33 %
Crystal grow
*PLUS
Method: microdialysis / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
250 mMcacodylate-HCl1drop
350 mMcacodylate-HCl1reservoir
40.5 Mammonium sulfate1reservoir

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Data collection

ReflectionResolution: 1.8→7 Å / Num. obs: 18656 / % possible obs: 98 % / Observed criterion σ(I): 3
Reflection
*PLUS
Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 15 201 1908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.07
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.15
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.15

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