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- PDB-6ri3: Dodecin from Streptomyces davaonensis -

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Basic information

Entry
Database: PDB / ID: 6ri3
TitleDodecin from Streptomyces davaonensis
Componentsdodecin
KeywordsFLAVOPROTEIN / Dodecin
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
Dodecin family protein
Similarity search - Component
Biological speciesStreptomyces davaonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPaithankar, K.S. / Bourdeaux, F. / Grininger, M. / Ludwig, P. / Mack, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFKZ 0316052A Germany
CitationJournal: Microbiology (Reading, Engl.) / Year: 2019
Title: Comparative biochemical and structural analysis of the flavin-binding dodecins from Streptomyces davaonensis and Streptomyces coelicolor reveals striking differences with regard to multimerization.
Authors: Bourdeaux, F. / Ludwig, P. / Paithankar, K. / Sander, B. / Essen, L.O. / Grininger, M. / Mack, M.
History
DepositionApr 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / 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
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_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)48,1136
Polymers48,1136
Non-polymers00
Water00
1
A: dodecin
B: dodecin
C: dodecin
D: dodecin
E: dodecin
F: dodecin

A: dodecin
B: dodecin
C: dodecin
D: dodecin
E: dodecin
F: dodecin


Theoretical massNumber of molelcules
Total (without water)96,22612
Polymers96,22612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area25320 Å2
ΔGint-72 kcal/mol
Surface area33770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.288, 72.288, 151.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 69 / Label seq-ID: 2 - 69

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
dodecin


Mass: 8018.866 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces davaonensis (bacteria) / Gene: BN159_1333 / Production host: Escherichia coli (E. coli) / References: UniProt: K4QXP8

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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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 10% (w/v) PEG-4000, 0.1 M NaOAc, pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16434 / % possible obs: 100 % / Redundancy: 11 % / Net I/σ(I): 28
Reflection shellResolution: 2.4→2.5 Å / Num. unique obs: 1694 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yiz

2yiz


Resolution: 2.4→36.17 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.705 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.295 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -5.3 %RANDOM
Rwork0.22 ---
obs-15514 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.4→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 0 0 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172934
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6334512
X-RAY DIFFRACTIONr_angle_other_deg1.2751.5836768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90722.432222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28315540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5731530
X-RAY DIFFRACTIONr_chiral_restr0.0670.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02738
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_it4.0044.2741626
X-RAY DIFFRACTIONr_mcbond_other4.0024.2711625
X-RAY DIFFRACTIONr_mcangle_it6.4066.3692022
X-RAY DIFFRACTIONr_mcangle_other6.4056.3732023
X-RAY DIFFRACTIONr_scbond_it4.5144.9111698
X-RAY DIFFRACTIONr_scbond_other4.5134.9051696
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2167.1492490
X-RAY DIFFRACTIONr_long_range_B_refined10.01146.763286
X-RAY DIFFRACTIONr_long_range_B_other10.0146.7913287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A18690.11
12B18690.11
21A18950.09
22C18950.09
31A18800.1
32D18800.1
41A18850.11
42E18850.11
51A19040.11
52F19040.11
61B19020.09
62C19020.09
71B18820.11
72D18820.11
81B18820.12
82E18820.12
91B18750.12
92F18750.12
101C18850.11
102D18850.11
111C19070.11
112E19070.11
121C19250.1
122F19250.1
131D18930.12
132E18930.12
141D18730.12
142F18730.12
151E18760.13
152F18760.13
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 51 -
Rwork0.303 1114 -
obs--100 %

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