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- PDB-1dak: DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION I... -

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Basic information

Entry
Database: PDB / ID: 1dak
TitleDETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE
ComponentsDETHIOBIOTIN SYNTHETASE
KeywordsLIGASE / PHOSHPORYL TRANSFER / BIOTIN BIOSYNTHESIS / KINETIC CRYSTALLOGRAPHY
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-DPU / PHOSPHATE ION / ATP-dependent dethiobiotin synthetase BioD 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.6 Å
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.
History
DepositionMar 31, 1998Processing site: BNL
Revision 1.0Apr 6, 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: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9116
Polymers24,0281
Non-polymers8835
Water3,891216
1
A: DETHIOBIOTIN SYNTHETASE
hetero molecules

A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,82312
Polymers48,0572
Non-polymers1,76610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6950 Å2
ΔGint-106 kcal/mol
Surface area16690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.680, 48.190, 61.070
Angle α, β, γ (deg.)90.00, 106.58, 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 DETHIOBIOTIN SYNTHETASE


Mass: 24028.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DPU / MIXED CARBAMIC PHOSPHORIC ACID ANHYDRIDE OF 7,8-DIAMINONONANIC ACID


Mass: 312.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H21N2O7P
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Details: drop contained 0.003ml of protein solution mixed with 0.074ml of well solution.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
3100 mM1reservoirMgAc
49-12 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.7606
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7606 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 86120 / % possible obs: 99 % / Redundancy: 3.2 % / Rsym value: 0.078 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.43 / % possible all: 92.4
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.43

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED

1dah


Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1505 5.1 %RANDOM
Rwork0.184 ---
obs-29418 99 %-
Displacement parametersBiso mean: 13.6 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 54 216 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.020.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8622
X-RAY DIFFRACTIONp_mcangle_it1.3353
X-RAY DIFFRACTIONp_scbond_it1.2272
X-RAY DIFFRACTIONp_scangle_it1.9493
X-RAY DIFFRACTIONp_plane_restr0.0165
X-RAY DIFFRACTIONp_chiral_restr0.0810.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor15.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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