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- PDB-5mji: Crystal Structure of RosB with bound intermediate OHC-RP (8-demet... -

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Basic information

Entry
Database: PDB / ID: 5mji
TitleCrystal Structure of RosB with bound intermediate OHC-RP (8-demethyl-8-formylriboflavin-5'-phosphate)
ComponentsBRAMP domain protein
KeywordsFLAVOPROTEIN / Flavodoxin-like / roseoflavin / electron transport
Function / homology
Function and homology information


8-demethyl-8-aminoriboflavin-5'-phosphate synthase / antibiotic metabolic process / transaminase activity / antibiotic biosynthetic process / oxidoreductase activity
Similarity search - Function
NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily
Similarity search - Domain/homology
Chem-7O6 / 8-demethyl-8-aminoriboflavin-5'-phosphate synthase
Similarity search - Component
Biological speciesStreptomyces davawensis JCM 4913 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKonjik, V. / Bruenle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Mack, M. / Ermler, U.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes.
Authors: Konjik, V. / Brunle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Ermler, U. / Mack, M.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRAMP domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3712
Polymers28,9001
Non-polymers4711
Water3,081171
1
A: BRAMP domain protein
hetero molecules

A: BRAMP domain protein
hetero molecules

A: BRAMP domain protein
hetero molecules

A: BRAMP domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4848
Polymers115,5994
Non-polymers1,8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+21
crystal symmetry operation10_775-x+2,-y+2,z1
crystal symmetry operation15_557y,x,-z+21
Buried area31480 Å2
ΔGint-131 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.470, 108.470, 178.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein BRAMP domain protein


Mass: 28899.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces davawensis JCM 4913 (bacteria)
Gene: BN159_7989 / Production host: Escherichia coli (E. coli) / References: UniProt: K4REZ6
#2: Chemical ChemComp-7O6 / [(2~{S},3~{R},4~{R})-5-[8-methanoyl-7-methyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-ium-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 471.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O10P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.3 M sodium formate, 25 % (v/v) Silver Bullet 49, 17 % (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36244 / % possible obs: 99.9 % / Redundancy: 10.7 % / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 2.12 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.806 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.2089 1823 5.03 %
Rwork0.1859 --
obs0.1871 36216 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 32 171 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092076
X-RAY DIFFRACTIONf_angle_d1.1222825
X-RAY DIFFRACTIONf_dihedral_angle_d20.0231236
X-RAY DIFFRACTIONf_chiral_restr0.061311
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.33651490.33482598X-RAY DIFFRACTION100
2.0541-2.11450.34391360.30012592X-RAY DIFFRACTION100
2.1145-2.18280.30631230.27512620X-RAY DIFFRACTION100
2.1828-2.26080.31391480.25812628X-RAY DIFFRACTION100
2.2608-2.35130.29341480.24222607X-RAY DIFFRACTION100
2.3513-2.45830.271440.21952585X-RAY DIFFRACTION100
2.4583-2.58790.22951330.19932625X-RAY DIFFRACTION100
2.5879-2.750.21971270.19112646X-RAY DIFFRACTION100
2.75-2.96230.20421350.18362646X-RAY DIFFRACTION100
2.9623-3.26030.21261580.17532639X-RAY DIFFRACTION100
3.2603-3.7320.17881420.15932665X-RAY DIFFRACTION100
3.732-4.70120.16021410.14662702X-RAY DIFFRACTION100
4.7012-46.81920.19761390.18582840X-RAY DIFFRACTION100

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