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- PDB-2vkg: COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS -

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Basic information

Entry
Database: PDB / ID: 2vkg
TitleCOMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
ComponentsDODECIN
KeywordsELECTRON TRANSPORT / BIOTECHNOLOGICAL APPLICATION OF DODECIN BINDING PROPERTIES / FLAVIN-DNA LIGAND HYBRID
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrininger, M. / Noell, G. / Trawoeger, S. / Sinner, E. / Oesterhelt, D.
CitationJournal: Biointerphases / Year: 2008
Title: Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified by Flavin-DNA Hybrid Linkers
Authors: Grininger, M. / Noell, G. / Trawoeger, S. / Sinner, E. / Oesterhelt, D.
History
DepositionDec 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: DODECIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2837
Polymers6,7221
Non-polymers5606
Water1,54986
1
A: DODECIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)87,39484
Polymers80,66812
Non-polymers6,72672
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation82_555-y,z,-x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation26_555-x,-y,z1
Buried area32730 Å2
ΔGint-587.9 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.030, 142.030, 142.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-1063-

NA

21A-1066-

CL

31A-1068-

SO4

41A-1068-

SO4

51A-2001-

HOH

61A-2011-

HOH

71A-2028-

HOH

81A-2036-

HOH

91A-2061-

HOH

101A-2086-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DODECIN


Mass: 6722.342 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-58,61-74 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LIGAND BOUND / Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: R1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 671) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HPW4

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Non-polymers , 6 types, 92 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CF4 / [4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid


Mass: 357.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 54 TO ALA
Nonpolymer detailsCOFC4_O5 (CF4): SYNTHETIC FLAVIN
Sequence detailsMUTATION OF E45A AND DELETION OF GLU50,GLU51(UNP GLU59, GLU60)

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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: 3.52 Å3/Da / Density % sol: 64.82 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MGCL2, 2 M NACL, 0.1 M HEPES, 30% PEG400, PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 107589 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCC

2ccc


Resolution: 1.8→19.75 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CRYSTALS WERE SOAKED WITH A FLAVIN-DNA HYBRID LIGAND. JUST THE ISOALLOXAZINE PART AS WELL AS THE ALIPHATIC PART IS VISIBLE IN DENSITY. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CRYSTALS WERE SOAKED WITH A FLAVIN-DNA HYBRID LIGAND. JUST THE ISOALLOXAZINE PART AS WELL AS THE ALIPHATIC PART IS VISIBLE IN DENSITY. BASES ARE NOT INCLUDED IN THE MODEL FOR THE LIGAND, BUT CAUSE SOME NOT EXPLAINED DENSITY IN BINDING POCKET.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 602 5.2 %RANDOM
Rwork0.192 ---
obs0.193 11077 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 35 86 594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.890.022524
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5472.001720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.112565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07826.2524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0691577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.859152
X-RAY DIFFRACTIONr_chiral_restr0.1120.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2171
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2354
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8781.5315
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6552512
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6953209
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.954.5207
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 39
Rwork0.269 796

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