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- PDB-1dts: CRYSTAL STRUCTURE OF AN ATP DEPENDENT CARBOXYLASE, DETHIOBIOTIN S... -

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Basic information

Entry
Database: PDB / ID: 1dts
TitleCRYSTAL STRUCTURE OF AN ATP DEPENDENT CARBOXYLASE, DETHIOBIOTIN SYNTHASE, AT 1.65 ANGSTROMS RESOLUTION
ComponentsDETHIOBIOTIN SYNTHETASE
KeywordsCYCLO-LIGASE
Function / homology
Function and homology information


dethiobiotin synthase activity / dethiobiotin synthase / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
CobQ/CobB/MinD/ParA nucleotide binding domain / Dethiobiotin synthase BioD / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 1.65 Å
AuthorsHuang, W. / Lindqvist, Y. / Schneider, G.
CitationJournal: 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
DepositionMar 28, 1995-
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DETHIOBIOTIN SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)23,7051
Polymers23,7051
Non-polymers00
Water3,405189
1
A: DETHIOBIOTIN SYNTHETASE

A: DETHIOBIOTIN SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)47,4102
Polymers47,4102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2790 Å2
ΔGint-12 kcal/mol
Surface area17840 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
Atom site foot note1: HOH 489 IS POSITIONED ON THE TWO-FOLD AXIS.
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

#1: Protein DETHIOBIOTIN SYNTHETASE


Mass: 23705.053 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 21608 / % possible obs: 84 % / Num. measured all: 34422 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.65→5.5 Å / σ(F): 1
RfactorNum. reflection
Rfree0.23 -
Rwork0.169 -
obs0.169 21134
Refinement stepCycle: LAST / Resolution: 1.65→5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 0 189 1849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.8
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.8

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