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

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Basic information

Entry
Database: PDB / ID: 2vkf
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: 1.7 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 / pdbx_struct_special_symmetry / 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)7,5047
Polymers6,7221
Non-polymers7826
Water1,54986
1
A: DODECIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)90,04884
Polymers80,66812
Non-polymers9,38072
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 area33160 Å2
ΔGint-599.6 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.704, 141.704, 141.704
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-1064-

CL

31A-1065-

SO4

41A-1065-

SO4

51A-2001-

HOH

61A-2004-

HOH

71A-2034-

HOH

81A-2060-

HOH

91A-2082-

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-CL / CHLORIDE ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CF2 / 2'-deoxy-5'-O-{[2-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)ethyl]carbamoyl}guanosine


Mass: 578.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26N10O7
#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 detailsCOFC2_O5 (CF2): NEW LIGAND, GUANOSIN ATTACHED VIA AN ALIPHATIC LINKER TO ISOALLOXAZINE
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: 3.41 Å3/Da / Density % sol: 63.64 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MGCL2, 2.0 M NACL, 0.1 M NA HEPES PH 7.5 AND 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.033
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.69→20 Å / Num. obs: 171130 / % possible obs: 95.4 % / Observed criterion σ(I): 3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.8
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.1 / % possible all: 79

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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: 1.7→19.03 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.474 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 703 5.2 %RANDOM
Rwork0.184 ---
obs0.186 12770 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 51 86 610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4582.041750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18226.2524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5841577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.926152
X-RAY DIFFRACTIONr_chiral_restr0.0950.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02409
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2190
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8431.5315
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5882512
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9853308
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7174.5237
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 44
Rwork0.267 730

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