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- PDB-1dad: DETHIOBIOTIN SYNTHETASE COMPLEXED WITH ADP -

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Basic information

Entry
Database: PDB / ID: 1dad
TitleDETHIOBIOTIN SYNTHETASE COMPLEXED WITH ADP
ComponentsDETHIOBIOTIN SYNTHETASE
KeywordsLIGASE / BIOTIN BIOSYNTHESIS / MAGNESIUM / ATP-BINDING
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
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent dethiobiotin synthetase BioD 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsHuang, W. / Jia, J. / Schneider, G. / Lindqvist, Y.
Citation
Journal: Biochemistry / Year: 1995
Title: Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
Authors: Huang, W. / Jia, J. / Gibson, K.J. / Taylor, W.S. / Rendina, A.R. / Schneider, G. / Lindqvist, Y.
#1: Journal: Structure / Year: 1994
Title: Crystal Structure of an ATP-Dependent Carboxylase, Dethiobiotin Synthetase, at 1.65 A Resolution
Authors: Huang, W. / Lindqvist, Y. / Schneider, G. / Gibson, K.J. / Flint, D. / Lorimer, G.
History
DepositionMay 8, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_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

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Assembly

Deposited unit
A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4552
Polymers24,0281
Non-polymers4271
Water2,504139
1
A: DETHIOBIOTIN SYNTHETASE
hetero molecules

A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9114
Polymers48,0572
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4250 Å2
ΔGint-23 kcal/mol
Surface area17580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.200, 49.200, 61.800
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

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Components

#1: Protein DETHIOBIOTIN SYNTHETASE / DTBS


Mass: 24028.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 34 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlenzyme1drop
20.2 M1reservoirCaCl2
313-18 %PEG80001reservoir
40.1 Mcacodylate 1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 3, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 25367 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.051
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 91245

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 1.6→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 23581
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 27 139 1858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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