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- PDB-4b2h: COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS -

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Basic information

Entry
Database: PDB / ID: 4b2h
TitleCOMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
ComponentsDODECIN
KeywordsFLAVOPROTEIN / BIOTECHNOLOGICAL APPLICATION OF DODECIN BINDING PROPERTIES / FLAVIN-DNA LIGAND HYBRID
Function / homology
Function and homology information


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: 1.6 Å
AuthorsYu, Y. / Heidel, B. / Parapugna, T.L. / Wenderhold-Reeb, S. / Song, B. / Schoenherr, H. / Grininger, M. / Noell, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: The Flavoprotein Dodecin as a Redox Probe for Electron Transfer Through DNA.
Authors: Yu, Y. / Heidel, B. / Parapugna, T.L. / Wenderhold-Reeb, S. / Song, B. / Schonherr, H. / Grininger, M. / Noll, G.
History
DepositionJul 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_special_symmetry ...pdbx_database_status / pdbx_struct_special_symmetry / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.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)8,7427
Polymers8,1971
Non-polymers5456
Water1,42379
1
A: DODECIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)104,90584
Polymers98,36312
Non-polymers6,54272
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation82_555-y,z,-x1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation26_555-x,-y,z1
Buried area33020 Å2
ΔGint-592.7 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.005, 142.005, 142.005
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-102-

SO4

21A-102-

SO4

31A-104-

NA

41A-106-

CL

51A-2031-

HOH

61A-2037-

HOH

71A-2051-

HOH

81A-2061-

HOH

91A-2078-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DODECIN


Mass: 8196.948 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LIGAND-BOUND FORM / Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: R1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 671) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0R5M0

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Non-polymers , 6 types, 85 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-C3F / 3-[7,8-dimethyl-2,4-bis(oxidanylidene)benzo[g]pteridin-10-yl]propylcarbamic acid


Mass: 343.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5O4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 45 TO ALA
Nonpolymer details[4-(7,8-DIMETHYL-2,4-DIOXO-3, 4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)PROPYL]CARBAMIC ACID (C3F): ...[4-(7,8-DIMETHYL-2,4-DIOXO-3, 4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)PROPYL]CARBAMIC ACID (C3F): ISOALLOXAZINE RING CONNECTED TO DNA VIA PROPYL CHAIN
Sequence detailsMUTATION OF E45A AND DELETION OF GLU50 AND GLU51 OE3073R AT HALOLEX DATABASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.44 Å3/Da / Density % sol: 72.28 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 20156 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 18 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 27.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 18 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCC

2ccc


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.897 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17759 862 5.2 %RANDOM
Rwork0.1665 ---
obs0.16709 15863 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.739 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 34 79 586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.02522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.7631.999719
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.192565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97626.2524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7521577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.386152
X-RAY DIFFRACTIONr_chiral_restr0.3020.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 53 -
Rwork0.224 1001 -
obs--100 %

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