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- PDB-2vyx: Crystal structure of the T. thermophilus dodecin W38F mutant -

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Basic information

Entry
Database: PDB / ID: 2vyx
TitleCrystal structure of the T. thermophilus dodecin W38F mutant
ComponentsTTHA1431
KeywordsFLAVOPROTEIN / DODECINS / COENZYME A / FLAVIN DIMER / HYPOTHETICAL PROTEIN / FLAVIN BINDING PROTEIN / PROTEIN BINDING PUTATIVE STORAGE PROTEIN
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
COENZYME A / FLAVIN MONONUCLEOTIDE / Dodecin
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEssen, L.-O. / Meissner, B.
CitationJournal: To be Published
Title: Ultrafast Charge Transfer Dynamics in Flavoprotein Dodecin
Authors: Gurzadyan, G.G. / Meissner, B. / Sander, B. / Essen, L.-O. / Michel-Beyerle, M.E.
History
DepositionJul 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / 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 / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 35-STRANDED BARREL THIS IS REPRESENTED BY A 36-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TTHA1431
B: TTHA1431
C: TTHA1431
D: TTHA1431
E: TTHA1431
F: TTHA1431
G: TTHA1431
H: TTHA1431
I: TTHA1431
J: TTHA1431
K: TTHA1431
L: TTHA1431
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,50241
Polymers92,65112
Non-polymers14,85129
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52810 Å2
ΔGint-136.5 kcal/mol
Surface area37480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.630, 98.550, 139.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.07151, -0.89315, -0.44403), (-0.49506, 0.35469, -0.79317), (0.86591, 0.27654, -0.4168)75.85555, 69.28524, 25.04398
2given(0.06158, -0.49886, 0.86449), (-0.88754, 0.36886, 0.27608), (-0.4566, -0.78427, -0.42004)7.94681, 35.55577, 99.7856
3given(-0.71093, -0.50061, -0.49394), (-0.49911, -0.13565, 0.85586), (-0.49545, 0.85498, -0.15342)121.67709, -15.71009, 86.83875
4given(0.61615, -0.30276, -0.72711), (0.5651, -0.47313, 0.67587), (-0.54865, -0.82733, -0.12043)59.66587, -65.62817, 89.55046
5given(-0.22007, 0.77293, -0.5951), (0.31323, 0.63374, 0.70729), (0.92383, -0.03076, -0.38158)1.45537, -0.54951, 0.14363
6given(0.62281, 0.17831, 0.76178), (0.16744, -0.9815, 0.09284), (0.76424, 0.06973, -0.64115)18.54745, -12.55949, 42.4423
7given(-0.45623, 0.85238, 0.25555), (-0.85278, -0.50084, 0.14808), (0.25421, -0.15037, 0.95539)67.23186, 41.09013, -11.79927
8given(0.61826, 0.56816, -0.5431), (-0.2805, -0.48598, -0.82773), (-0.73422, 0.66409, -0.14109)49.10332, 59.99199, 99.66828
9given(-0.90387, 0.32569, -0.27739), (0.32938, 0.11604, -0.93704), (-0.273, -0.93833, -0.21217)120.41289, 31.02123, 79.07696
10given(-0.22846, 0.33669, 0.91348), (0.78294, 0.62121, -0.03316), (-0.57863, 0.70763, -0.40553)20.77888, -41.81575, 104.67992
11given(-0.45168, -0.84861, 0.27541), (0.85068, -0.50269, -0.15377), (0.26893, 0.16484, 0.94895)67.64282, -38.26821, -12.76519

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
TTHA1431 / DODECIN


Mass: 7720.895 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q5SIE3

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Non-polymers , 5 types, 561 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN B, TRP 38 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN B, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN C, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN D, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN E, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN F, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN G, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN H, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN I, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN J, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN K, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN L, TRP 38 TO PHE
Nonpolymer detailsCOENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE ...COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE (FMN): FMN IS BOUND AS DIMERS ALONG THE TWOFOLD SYMMETRY AXES

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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: 2.56 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.2, 22.5 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→9.99 Å / Num. obs: 178447 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.7
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V18

2v18


Resolution: 1.5→9.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.376 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 7159 4.9 %RANDOM
Rwork0.218 ---
obs0.22 138426 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 953 532 7811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227469
X-RAY DIFFRACTIONr_bond_other_d0.0020.024954
X-RAY DIFFRACTIONr_angle_refined_deg1.4232.13610174
X-RAY DIFFRACTIONr_angle_other_deg0.889312076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.85923.684304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9461560
X-RAY DIFFRACTIONr_chiral_restr0.0730.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021346
X-RAY DIFFRACTIONr_nbd_refined0.1770.21148
X-RAY DIFFRACTIONr_nbd_other0.1990.25551
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23445
X-RAY DIFFRACTIONr_nbtor_other0.0830.24031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2603
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7271.53979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36726335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.76333898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0584.53832
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.38 501
Rwork0.352 10008

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