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- PDB-6r1e: Structure of dodecin from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 6r1e
TitleStructure of dodecin from Streptomyces coelicolor
Componentsdodecin
KeywordsFLAVOPROTEIN / flavin storage / dodecamer / protein complex
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 domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEssen, L.-O. / Sander, B.
CitationJournal: Microbiology (Reading, Engl.) / Year: 2019
Title: Comparative biochemical and structural analysis of the flavin-binding dodecins fromStreptomyces davaonensisandStreptomyces coelicolorreveals striking differences with regard to multimerization.
Authors: Bourdeaux, F. / Ludwig, P. / Paithankar, K. / Sander, B. / Essen, L.O. / Grininger, M. / Mack, M.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 7, 2022Group: Database references / Refinement description / Category: database_2 / refine / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_ref_seq_dif.details
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,38926
Polymers31,6834
Non-polymers5,70622
Water1,62190
1
A: dodecin
B: dodecin
C: dodecin
D: dodecin
hetero molecules

A: dodecin
B: dodecin
C: dodecin
D: dodecin
hetero molecules

A: dodecin
B: dodecin
C: dodecin
D: dodecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,16778
Polymers95,05012
Non-polymers17,11766
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area47750 Å2
ΔGint-651 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.945, 92.945, 227.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-105-

SO4

21B-105-

SO4

31B-106-

SO4

41B-106-

SO4

51C-106-

SO4

61C-106-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 15 - 84 / Label seq-ID: 2 - 71

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
dodecin


Mass: 7920.802 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-formylated N-terminus
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Gene: SCO0915 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Gold(DE3) / References: UniProt: Q9RCZ5

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Non-polymers , 6 types, 112 molecules

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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#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.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 10% PEG4000, 0.1 M NaOAc, 0.2 M AS, 16.5 mg/mL ScDodecin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2007
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.6→11.9 Å / Num. all: 66956 / Num. obs: 11644 / % possible obs: 99 % / Redundancy: 5.75 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.6
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.72 / Num. unique obs: 549 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YIZ

2yiz


Resolution: 2.6→11.86 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.074 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.907 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24286 277 2.3 %RANDOM
Rwork0.19753 ---
obs0.19867 11583 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.755 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→11.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 354 90 2676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192624
X-RAY DIFFRACTIONr_bond_other_d0.0010.022252
X-RAY DIFFRACTIONr_angle_refined_deg1.8472.0783604
X-RAY DIFFRACTIONr_angle_other_deg0.88735184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.29923.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38215384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7751524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02548
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_it2.5855.1331124
X-RAY DIFFRACTIONr_mcbond_other2.5865.131123
X-RAY DIFFRACTIONr_mcangle_it4.0587.6691396
X-RAY DIFFRACTIONr_mcangle_other4.0577.6731397
X-RAY DIFFRACTIONr_scbond_it2.6035.3271500
X-RAY DIFFRACTIONr_scbond_other2.6115.3221477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9617.9152173
X-RAY DIFFRACTIONr_long_range_B_refined6.48954.2843140
X-RAY DIFFRACTIONr_long_range_B_other6.48654.2213128
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)
11A20740.03
12B20740.03
21A20850
22C20850
31A20740.04
32D20740.04
41B20740.03
42C20740.03
51B20690.04
52D20690.04
61C20740.04
62D20740.04
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.22 853 -
obs--100 %

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