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- PDB-2vxa: H. halophila dodecin in complex with riboflavin -

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Basic information

Entry
Database: PDB / ID: 2vxa
TitleH. halophila dodecin in complex with riboflavin
ComponentsDODECIN
KeywordsFLAVOPROTEIN / DODECIN / FLAVIN / RIBOFLAVIN / LUMICHROME / ARCHAEA
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 speciesHALORHODOSPIRA HALOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGrininger, M. / Staudt, H. / Johansson, P. / Wachtveitl, J. / Oesterhelt, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Dodecin is the Key Player in Flavin Homeostasis of Archaea.
Authors: Grininger, M. / Staudtb, H. / Johansson, P. / Wachtveitl, J. / Oesterhelt, D.
History
DepositionJul 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,31848
Polymers95,95112
Non-polymers5,36736
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38550 Å2
ΔGint-333.07 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.760, 100.510, 100.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: RBF / End label comp-ID: RBF / Refine code: 1 / Auth seq-ID: 5 - 200 / Label seq-ID: 5

Dom-IDAuth asym-IDLabel asym-ID
1AA - M
2BB - P
3CC - S
4DD - V
5EE - Z
6FF - DA
7GG - FA
8HH - KA
9II - MA
10JJ - PA
11KK - SA
12LL - VA

NCS oper:
IDCodeMatrixVector
1given(-0.47032, 0.854, 0.22243), (-0.67441, -0.18526, -0.71474), (-0.56918, -0.48617, 0.66308)-3.52739, -33.76199, -18.07508
2given(-0.48307, -0.67006, -0.56361), (0.84977, -0.20364, -0.48623), (0.21103, -0.71383, 0.66777)-35.01495, -12.57584, -11.71265
3given(-0.05609, -0.99842, -0.00427), (0.03334, -0.00615, 0.99943), (-0.99787, 0.05591, 0.03363)-51.25121, -55.27319, 6.45628
4given(0.6857, 0.1416, 0.71398), (-0.59729, -0.45115, 0.6631), (0.41601, -0.88114, -0.22478)-17.54269, -73.26902, 7.26337
5given(-0.82453, 0.22855, 0.5176), (0.20088, -0.73695, 0.64541), (0.52896, 0.63614, 0.56173)-37.02407, -67.73959, 40.17754
6given(-0.17106, 0.72732, -0.66464), (0.49381, 0.64703, 0.58095), (0.85258, -0.22883, -0.46984)18.25812, -16.27037, 41.77868
7given(-0.03664, 0.03604, -0.99868), (-0.99932, 0.00343, 0.03679), (0.00476, 0.99934, 0.03589)6.02591, -50.91081, 54.88728
8given(0.56239, 0.44744, -0.69536), (0.44431, -0.87275, -0.20223), (-0.69736, -0.19522, -0.68963)22.96303, -48.2522, 20.52251
9given(-0.17784, 0.48897, 0.85398), (0.74172, 0.63691, -0.21022), (-0.6467, 0.59603, -0.47595)-24.99867, 6.38893, 42.15828
10given(-0.74285, -0.6463, 0.17455), (-0.6463, 0.62435, -0.43873), (0.17457, -0.43872, -0.8815)-56.14083, -13.3762, 32.54986
11given(0.68141, -0.59549, 0.42553), (0.14756, -0.45769, -0.87678), (0.71688, 0.66024, -0.224)-34.88295, -24.26327, 62.71323

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Components

#1: Protein
DODECIN


Mass: 7995.937 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALORHODOSPIRA HALOPHILA (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1WUH0
#2: Chemical
ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl

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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: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5
Details: 100MM NACL, 100MM KCL, 0.1M ECTOINE, 1MM MGCL2, 20MM HEPES PH 7.5

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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: Oct 14, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 26701 / % possible obs: 98.6 % / Observed criterion σ(I): 3.5 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.76 / % possible all: 95.7

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Processing

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

2ccb


Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.864 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1370 5 %RANDOM
Rwork0.251 ---
obs0.253 25902 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6267 0 348 0 6615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9659208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.2422.985325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.164151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.4791560
X-RAY DIFFRACTIONr_chiral_restr0.1370.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.22510
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24522
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5410.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4120.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.011.53888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71726265
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86132859
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1764.52943
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 534 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.050.05
8Htight positional0.050.05
9Itight positional0.050.05
10Jtight positional0.050.05
11Ktight positional0.050.05
12Ltight positional0.060.05
1Atight thermal0.140.5
2Btight thermal0.120.5
3Ctight thermal0.180.5
4Dtight thermal0.120.5
5Etight thermal0.130.5
6Ftight thermal0.140.5
7Gtight thermal0.130.5
8Htight thermal0.120.5
9Itight thermal0.120.5
10Jtight thermal0.150.5
11Ktight thermal0.150.5
12Ltight thermal0.160.5
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 111 -
Rwork0.36 1839 -
obs--99.85 %

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