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- PDB-4b2j: COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS -

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Basic information

Entry
Database: PDB / ID: 4b2j
TitleCOMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
ComponentsDODECIN
KeywordsFLAVOPROTEIN / INCORPORATION / INCORPORATION OF ARTIFICIAL (NON-CANONICAL) AMINO ACIDS / PROTEIN REACTION CONTROL
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
RIBOFLAVIN / Dodecin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStaudt, H. / Hoesl, M. / Dreuw, A. / Serdjukow, S. / Oesterhelt, D. / Budisa, N. / Wachtveitl, J. / Grininger, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Directed Manipulation of a Flavoprotein Photocycle.
Authors: Staudt, H. / Hoesl, M.G. / Dreuw, A. / Serdjukow, S. / Oesterhelt, D. / Budisa, N. / Wachtveitl, J. / Grininger, M.
History
DepositionJul 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Dec 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: DODECIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1117
Polymers8,5311
Non-polymers5796
Water1,56787
1
A: DODECIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)109,32884
Polymers102,37412
Non-polymers6,95472
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 area36160 Å2
ΔGint-615 kcal/mol
MethodPISA
Unit cell
Length a, b, c (Å)142.900, 142.900, 142.900
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-103-

NA

21A-104-

CL

31A-300-

SO4

41A-300-

SO4

51A-2001-

HOH

61A-2038-

HOH

71A-2061-

HOH

81A-2062-

HOH

91A-2083-

HOH

101A-2084-

HOH

111A-2086-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DODECIN


Mass: 8531.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TRYPTOPHAN 36 EXCHANGED BY 4F-FLUOROTRYPTOPHAN, RIBOFLAVIN BOUND
Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: R1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 671) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B0R5M0

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Non-polymers , 6 types, 93 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-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, PEG 400 30% (V/V), 2.5 M NACL, 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 10355 / % possible obs: 99.9 % / Observed criterion σ(I): 4 / Redundancy: 14 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 14 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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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: 1.9→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.82 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18639 538 5.2 %RANDOM
Rwork0.16509 ---
obs0.16624 9807 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.198 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 0 27 87 610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02530
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8512.038724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13627.03727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5541582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.503152
X-RAY DIFFRACTIONr_chiral_restr0.2690.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02402
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 28 -
Rwork0.219 609 -
obs--100 %

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