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- PDB-1dam: DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGAN... -

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Basic information

Entry
Database: PDB / ID: 1dam
TitleDETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM
ComponentsPROTEIN (DETHIOBIOTIN SYNTHETASE)
KeywordsLIGASE / BIOTIN BIOSYNTHESIS / MAGNESIUM / ATP-BINDING / PHOSPHORYL TRANSFER
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 / OTHER / 1.8 Å resolution
AuthorsKaeck, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y.
Citation
Journal: Protein Sci. / Year: 1998
Title: Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
Authors: Kack, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Snapshot of a Phosphorylated Substrate Intermediate by Kinetic Crystallography
Authors: Kaeck, H. / Gibson, K.J. / Schneider, G. / Lindqvist, Y.
#2: 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: Aug 31, 1998 / Release: Jan 13, 1999
RevisionDateData content typeGroupCategoryProviderType
1.0Jan 13, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3Apr 6, 2016Structure modelNon-polymer description
1.4Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (DETHIOBIOTIN SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8136
Polyers24,0281
Non-polymers7855
Water3,585199
1
A: PROTEIN (DETHIOBIOTIN SYNTHETASE)
hetero molecules

A: PROTEIN (DETHIOBIOTIN SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,62712
Polyers48,0572
Non-polymers1,57010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)6610
ΔGint (kcal/M)-96
Surface area (Å2)16850
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)72.700, 48.900, 61.100
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide PROTEIN (DETHIOBIOTIN SYNTHETASE) / E.C.6.3.3.3 LIGASE / DTBS


Mass: 24028.289 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase

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Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 1 / Formula: C10H18N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Formula: H2O / Water

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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: 2.16 / Density percent sol: 34 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
1100 mMmagnesium acetate1reservoircan be replaced by MgCl2
29-11 %PEG80001reservoir
3100 mMcacodylate1reservoir
430 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Collection date: Jul 1, 1996
RadiationMonochromator: GRAPHITE / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 3 Å / Number obs: 17046 / Rsym value: 0.044 / NetI over sigmaI: 18.1 / Redundancy: 2.5 % / Percent possible obs: 90.6
Reflection shellHighest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 3.3 / Rsym value: 0.337 / Percent possible all: 86.1
Reflection
*PLUS
Number measured all: 42816 / Rmerge I obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Percent possible obs: 86.1 / Rmerge I obs: 0.337

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: OTHER / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 15.6 Å2
Least-squares processR factor R free: 0.233 / R factor R work: 0.18 / Highest resolution: 1.8 Å / Lowest resolution: 2 Å / Number reflection R free: 789 / Number reflection obs: 18683 / Percent reflection R free: 4.7 / Percent reflection obs: 90.6
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1692 / Nucleic acid: 0 / Ligand: 49 / Solvent: 199 / Total: 1940
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.020
X-RAY DIFFRACTIONp_angle_d0.0240.040
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0682.000
X-RAY DIFFRACTIONp_mcangle_it1.6583.000
X-RAY DIFFRACTIONp_scbond_it1.3102.000
X-RAY DIFFRACTIONp_scangle_it2.1013.000
X-RAY DIFFRACTIONp_plane_restr0.0183
X-RAY DIFFRACTIONp_chiral_restr0.085
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2500.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.167.3
X-RAY DIFFRACTIONp_planar_tor3.37.0
X-RAY DIFFRACTIONp_staggered_tor18.815.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor15.0
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 15.6 Å2
Least-squares process
*PLUS
R factor R work: 0.18 / R factor obs: 0.18 / Highest resolution: 1.8 Å / Percent reflection R free: 4.7

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