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- PDB-1mog: Crystal structure of H. salinarum dodecin -

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Basic information

Entry
Database: PDB / ID: 1mog
TitleCrystal structure of H. salinarum dodecin
ComponentsDodecin
KeywordsUNKNOWN FUNCTION / binding site for dimerized riboflavin / 23-symmetric dodecamer
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
RIBOFLAVIN / Dodecin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsBieger, B. / Essen, L.-O. / Oesterhelt, D.
CitationJournal: Structure / Year: 2003
Title: Crystal Structure of Halophilic Dodecin: A Novel, Dodecameric Flavin Binding Protein from Halobacterium salinarum
Authors: Bieger, B. / Essen, L.-O. / Oesterhelt, D.
History
DepositionSep 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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

Downloads & links

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Assembly

Deposited unit
A: Dodecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8307
Polymers7,3111
Non-polymers5196
Water1,76598
1
A: Dodecin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)93,95784
Polymers87,73012
Non-polymers6,22672
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation82_555-y,z,-x1
Buried area36940 Å2
ΔGint-370 kcal/mol
Surface area26010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)141.890, 141.890, 141.890
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-203-

NA

21A-204-

CL

31A-205-

CL

41A-206-

HOH

51A-208-

HOH

61A-222-

HOH

71A-236-

HOH

81A-250-

HOH

91A-264-

HOH

101A-300-

HOH

111A-302-

HOH

DetailsThe biological assembly is a dodecamer generated from the monomer in the asymmetric unit by the operations: X,Y,Z Z,X,Y Y,Z,X -X,-Y,Z -Z,-X,Y -Y,-Z,X X,-Y,-Z Z,-X,-Y Y,-Z,-X -X,Y,-Z -Z,X,-Y -Y,Z,-X

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dodecin / VNG1446H


Mass: 7310.863 Da / Num. of mol.: 1 / Fragment: residues 10-77 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / References: UniProt: Q9HPW4

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Non-polymers , 5 types, 104 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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, magnesium chloride, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-15 mg/mlprotein1drop
230 %PEG4001reservoir
30.2 M1reservoirMgCl2
40.1 MHEPES1reservoirpH7.5
51.0 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 14027 / Num. obs: 14027 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 38.3
Reflection shellResolution: 1.7→1.72 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 116286
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.7→14.88 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1250 9.1 %RANDOM
Rwork0.18 ---
all0.18 13753 --
obs0.18 13753 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.0684 Å2 / ksol: 0.445967 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms515 0 32 98 645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it2.022
X-RAY DIFFRACTIONc_mcangle_it3.232.5
X-RAY DIFFRACTIONc_scbond_it3.213
X-RAY DIFFRACTIONc_scangle_it4.953.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 226 10 %
Rwork0.193 2026 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LUM.PARAMLUM.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 9 % / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22
LS refinement shell
*PLUS
Rfactor Rfree: 0.214

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