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- PDB-1a82: DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBST... -

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Basic information

Entry
Database: PDB / ID: 1a82
TitleDETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID
ComponentsDETHIOBIOTIN SYNTHETASE
KeywordsBIOTIN BIOSYNTHESIS / PHOSPHORYL TRANSFER / LIGASE
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 / DIFFERENCE FOURIER / 1.8 Å resolution
AuthorsKaeck, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Authors: Kack, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 31, 1998 / Release: May 11, 1999
RevisionDateData content typeGroupProviderType
1.0May 11, 1999Structure 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)24,7484
Polyers24,0281
Non-polymers7203
Water3,945219
1
A: DETHIOBIOTIN SYNTHETASE
hetero molecules

A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4968
Polyers48,0572
Non-polymers1,4406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)6090
ΔGint (kcal/M)-20
Surface area (Å2)16920
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)72.900, 47.900, 60.900
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide DETHIOBIOTIN SYNTHETASE


Mass: 24028.289 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Cellular location: CYTOPLASM / Genus (production host): Escherichia / Cellular location (production host): CYTOPLASM / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-DNN / 7,8-DIAMINO-NONANOIC ACID


Mass: 188.267 Da / Num. of mol.: 1 / Formula: C9H20N2O2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.15 / Density percent sol: 43 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop contained 0.003ml of protein solution mixed with 0.074ml of well solution.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
130 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
3100 mM1reservoirMgAc
49-12 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Feb 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 11.9 Å2 / D resolution high: 1.8 Å / D resolution low: 2 Å / Number obs: 18671 / Rsym value: 0.03 / NetI over sigmaI: 25.6 / Redundancy: 2.5 % / Percent possible obs: 98.7
Reflection shellHighest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 7 / Rsym value: 0.116 / Redundancy: 2.4 % / Percent possible all: 93.5
Reflection
*PLUS
Number measured all: 47020 / Rmerge I obs: 0.03
Reflection shell
*PLUS
Percent possible obs: 93.5 / Rmerge I obs: 0.116

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 9 Å2
Least-squares processR factor R free: 0.246 / R factor R free error: 0.008 / R factor R work: 0.19 / R factor obs: 0.19 / Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Number reflection R free: 903 / Number reflection obs: 17659 / Percent reflection R free: 5 / Percent reflection obs: 98.7
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 1692 / Nucleic acid: 0 / Ligand: 45 / Solvent: 219 / Total: 1956
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
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_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
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
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.2461 / R factor R free error: 0.024 / R factor R work: 0.1896 / Lowest resolution: 1.86 Å / Number reflection R free: 101 / Number reflection R work: 1678 / Total number of bins used: 10 / Percent reflection R free: 6 / Percent reflection obs: 93.5
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM11.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.19
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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