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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 / 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
ADENOSINE-5'-DIPHOSPHATE / Chem-DTB / PHOSPHATE ION / ATP-dependent dethiobiotin synthetase BioD 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
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.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 6, 2016Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Polymers24,0281
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
Polymers48,0572
Non-polymers1,57010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6610 Å2
ΔGint-96 kcal/mol
Surface area16850 Å2
MethodPISA, PQS
Unit cell
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-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 24028.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / 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 / Source method: obtained synthetically / Formula: C10H18N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.16 Å3/Da / Density % sol: 34 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common 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 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 17046 / % possible obs: 90.6 % / Redundancy: 2.5 % / Rsym value: 0.044 / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.337 / % possible all: 86.1
Reflection
*PLUS
Num. measured all: 42816 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 86.1 % / Rmerge(I) obs: 0.337

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 789 4.7 %RANDOM
Rwork0.18 ---
obs-18683 90.6 %-
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 49 199 1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0682
X-RAY DIFFRACTIONp_mcangle_it1.6583
X-RAY DIFFRACTIONp_scbond_it1.312
X-RAY DIFFRACTIONp_scangle_it2.1013
X-RAY DIFFRACTIONp_plane_restr0.0183
X-RAY DIFFRACTIONp_chiral_restr0.085
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1670.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor18.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 0 / % reflection Rfree: 4.7 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.6 Å2

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