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- PDB-5mld: Crystal Structure of RosB with bound intermediate AFP (8-demethyl... -

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Basic information

Entry
Database: PDB / ID: 5mld
TitleCrystal Structure of RosB with bound intermediate AFP (8-demethyl-8-aminoriboflavin-5'-phosphate)
ComponentsBRAMP domain protein
KeywordsELECTRON TRANSPORT / Flavodoxin-like / roseoflavin / vitamin B2
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
8-demethyl-8-aminoriboflavin-5'-phosphate / 8-demethyl-8-aminoriboflavin-5'-phosphate synthase
Similarity search - Component
Biological speciesStreptomyces davawensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKonjik, V. / Bruenle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Mack, M. / Ermler, U.
CitationJournal: To be published
Title: The crystal structure of RosB gives insights into the reaction mechanism of this first known member of a new family of flavodoxin-like enzymes
Authors: Konjik, V. / Bruenle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Mack, M. / Ermler, U.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
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
B: BRAMP domain protein
C: BRAMP domain protein
D: BRAMP domain protein
E: BRAMP domain protein
F: BRAMP domain protein
G: BRAMP domain protein
H: BRAMP domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,84816
Polymers231,1988
Non-polymers3,6518
Water32,1391784
1
A: BRAMP domain protein
B: BRAMP domain protein
C: BRAMP domain protein
D: BRAMP domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4248
Polymers115,5994
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31070 Å2
ΔGint-121 kcal/mol
Surface area31650 Å2
MethodPISA
2
E: BRAMP domain protein
F: BRAMP domain protein
G: BRAMP domain protein
H: BRAMP domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4248
Polymers115,5994
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31280 Å2
ΔGint-117 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.490, 71.130, 214.800
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
BRAMP domain protein / 8-demethyl-8-aminoriboflavin-5'-phosphate synthase (RosB)


Mass: 28899.688 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces davawensis (bacteria) / Gene: BN159_7989 / Production host: Escherichia coli (E. coli) / References: UniProt: K4REZ6
#2: Chemical
ChemComp-8DP / 8-demethyl-8-aminoriboflavin-5'-phosphate


Mass: 456.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C16H19N5O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1784 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.3 M sodium formate, 0.1 M potassium chloride, 17 % (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 202389 / % possible obs: 92.9 % / Redundancy: 10.7 % / Rsym value: 0.106 / Net I/σ(I): 15.36

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.7→47.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 10149 5.01 %
Rwork0.174 --
obs0.1759 202379 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15960 0 248 1784 17992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716710
X-RAY DIFFRACTIONf_angle_d0.95522755
X-RAY DIFFRACTIONf_dihedral_angle_d15.7639953
X-RAY DIFFRACTIONf_chiral_restr0.0552497
X-RAY DIFFRACTIONf_plane_restr0.0052952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.37432020.34613826X-RAY DIFFRACTION56
1.7193-1.73950.37632510.34254363X-RAY DIFFRACTION63
1.7395-1.76070.33852890.31044634X-RAY DIFFRACTION70
1.7607-1.7830.34892700.30665510X-RAY DIFFRACTION79
1.783-1.80650.34033020.2816321X-RAY DIFFRACTION93
1.8065-1.83120.30493790.26546509X-RAY DIFFRACTION95
1.8312-1.85740.33240.25226528X-RAY DIFFRACTION95
1.8574-1.88510.28083560.24916476X-RAY DIFFRACTION95
1.8851-1.91460.30143200.24856651X-RAY DIFFRACTION95
1.9146-1.9460.27953210.23056482X-RAY DIFFRACTION96
1.946-1.97950.25873490.22876628X-RAY DIFFRACTION96
1.9795-2.01550.28563080.21956650X-RAY DIFFRACTION96
2.0155-2.05430.25683330.20046559X-RAY DIFFRACTION96
2.0543-2.09620.22943750.19036595X-RAY DIFFRACTION96
2.0962-2.14180.23513650.19116638X-RAY DIFFRACTION97
2.1418-2.19160.25793530.18556670X-RAY DIFFRACTION97
2.1916-2.24640.22813600.17646599X-RAY DIFFRACTION97
2.2464-2.30720.22314170.17416658X-RAY DIFFRACTION97
2.3072-2.37510.22263370.18196657X-RAY DIFFRACTION97
2.3751-2.45170.24413360.17876785X-RAY DIFFRACTION97
2.4517-2.53930.24053710.17076666X-RAY DIFFRACTION98
2.5393-2.6410.22023760.17196767X-RAY DIFFRACTION98
2.641-2.76120.22893550.1696768X-RAY DIFFRACTION98
2.7612-2.90670.21333070.16686824X-RAY DIFFRACTION98
2.9067-3.08880.20343220.16746864X-RAY DIFFRACTION98
3.0888-3.32730.19813930.15726774X-RAY DIFFRACTION99
3.3273-3.6620.17853740.14416841X-RAY DIFFRACTION99
3.662-4.19160.16283660.13346941X-RAY DIFFRACTION99
4.1916-5.27990.15744030.13346893X-RAY DIFFRACTION99
5.2799-47.55910.17093350.16317153X-RAY DIFFRACTION99

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