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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 / homologyDethiobiotin synthase BioD / P-loop containing nucleoside triphosphate hydrolase / CobQ/CobB/MinD/ParA nucleotide binding domain / dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol / ATP-dependent dethiobiotin synthetase BioD 1
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / 1.6 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 8, 1995 / Release: Jun 20, 1996
RevisionDateData content typeGroupProviderType
1.0Jun 20, 1996Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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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
Polyers24,0281
Non-polymers4271
Water2,504139
1
A: DETHIOBIOTIN SYNTHETASE
hetero molecules

A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9114
Polyers48,0572
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)4250
ΔGint (kcal/M)-23
Surface area (Å2)17580
MethodPISA,PQS
Unit cell
γ
α
β
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-MC 1 2 1

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Components

#1: Protein/peptide DETHIOBIOTIN SYNTHETASE / DTBS


Mass: 24028.289 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / 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 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Formula: H2O / Water

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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 / Density percent sol: 34 %
Crystal grow
*PLUS
Temp: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
120 mg/mlenzyme1drop
20.2 M1reservoirCaCl2
313-18 %PEG80001reservoir
40.1 Mcacodylate 1reservoir

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Data collection

SourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Collection date: May 3, 1994
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber obs: 25367 / Observed criterion sigma I: 1 / Rmerge I obs: 0.051 / Redundancy: 3.6 % / Percent possible obs: 87
Reflection
*PLUS
D resolution high: 1.6 Å / Number measured all: 91245

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefineSigma F: 1
Displacement parametersB iso mean: 27.1 Å2
Least-squares processR factor R work: 0.183 / R factor obs: 0.183 / Highest resolution: 1.6 Å / Lowest resolution: 6 Å / Number reflection obs: 23581
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 1692 / Nucleic acid: 0 / Ligand: 27 / Solvent: 139 / Total: 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
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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