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- PDB-1byi: STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1byi
TitleSTRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION
ComponentsDETHIOBIOTIN SYNTHASE
KeywordsLIGASE / BIOTIN SYNTHESIS / CYCLO-LIGASE
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
ATP-dependent dethiobiotin synthetase BioD 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsSandalova, T. / Schneider, G. / Kaeck, H. / Lindqvist, Y.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of dethiobiotin synthetase at 0.97 A resolution.
Authors: Sandalova, T. / Schneider, G. / Kack, H. / 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
DepositionOct 15, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DETHIOBIOTIN SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,0281
Polymers24,0281
Non-polymers00
Water7,260403
1
A: DETHIOBIOTIN SYNTHASE

A: DETHIOBIOTIN SYNTHASE


Theoretical massNumber of molelcules
Total (without water)48,0572
Polymers48,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2800 Å2
ΔGint-12 kcal/mol
Surface area18630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.447, 47.812, 61.202
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-581-

HOH

31A-582-

HOH

41A-656-

HOH

51A-697-

HOH

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Components

#1: Protein DETHIOBIOTIN SYNTHASE


Mass: 24028.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 6 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
250 mMcacodylate-HCl1drop
350 mMcacodylate-HCl1reservoir
40.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9082
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9082 Å / Relative weight: 1
ReflectionResolution: 0.97→15 Å / Num. obs: 116232 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 54.4
Reflection shellResolution: 0.97→0.98 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.245 / % possible all: 94.3
Reflection
*PLUS
Num. measured all: 494742
Reflection shell
*PLUS
% possible obs: 94.3 % / Rmerge(I) obs: 0.245

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Processing

Software
NameClassification
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DTS

1dts


Resolution: 0.97→15 Å / Num. parameters: 20493 / Num. restraintsaints: 25635 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
obs0.1158 -98.5 %
all-116232 -
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 79 / Occupancy sum hydrogen: 1684.4 / Occupancy sum non hydrogen: 2075
Refinement stepCycle: LAST / Resolution: 0.97→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 0 403 2095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.149
X-RAY DIFFRACTIONs_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.075
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.089
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.078

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