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- PDB-6xbc: Crystal structure of Streptomyces sviceus SsDesB -

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Basic information

Entry
Database: PDB / ID: 6xbc
TitleCrystal structure of Streptomyces sviceus SsDesB
ComponentsMonooxigenase
KeywordsFLAVOPROTEIN / flavin-dependent monooxygenase / N-hydroxylase / desferrioxamine biosynthesis
Function / homologyL-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / L-lysine N6-monooxygenase MbtG
Function and homology information
Biological speciesStreptomyces sviceus ATCC 29083 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.863 Å
AuthorsLountos, G.T. / Giddings, L.A. / Waugh, D.S.
CitationJournal: Plos One / Year: 2021
Title: Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus.
Authors: Giddings, L.A. / Lountos, G.T. / Kim, K.W. / Brockley, M. / Needle, D. / Cherry, S. / Tropea, J.E. / Waugh, D.S.
History
DepositionJun 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monooxigenase
B: Monooxigenase
C: Monooxigenase
D: Monooxigenase
E: Monooxigenase
F: Monooxigenase
G: Monooxigenase
H: Monooxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,22016
Polymers385,9358
Non-polymers6,2848
Water00
1
A: Monooxigenase
B: Monooxigenase
C: Monooxigenase
D: Monooxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1108
Polymers192,9684
Non-polymers3,1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-160 kcal/mol
Surface area60750 Å2
MethodPISA
2
E: Monooxigenase
F: Monooxigenase
G: Monooxigenase
H: Monooxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1108
Polymers192,9684
Non-polymers3,1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23350 Å2
ΔGint-152 kcal/mol
Surface area60820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.046, 151.174, 141.401
Angle α, β, γ (deg.)90.000, 91.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Monooxigenase


Mass: 48241.914 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sviceus ATCC 29083 (bacteria)
Gene: SSEG_08523 / Plasmid: pGL3070 / Production host: Escherichia coli (E. coli) / References: UniProt: B5HNG5
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M NaCl, 20% w/v PEG3350, 10 mM taurine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→50 Å / Num. obs: 78957 / % possible obs: 98.7 % / Redundancy: 3.2 % / CC1/2: 0.996 / CC star: 0.962 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Rsym value: 0.066 / Net I/σ(I): 2.2
Reflection shellResolution: 2.86→2.9 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3917 / CC1/2: 0.86 / CC star: 0.962 / Rpim(I) all: 0.288 / Rrim(I) all: 0.537 / Rsym value: 0.451

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O8R

5o8r


Resolution: 2.863→39.119 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 3617 4.92 %
Rwork0.1991 69929 -
obs0.202 73546 91.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.86 Å2 / Biso mean: 47.7947 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 2.863→39.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26698 0 424 0 27122
Biso mean--49.23 --
Num. residues----3325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8632-2.90080.3975670.2898147251
2.9008-2.94050.336680.2697171758
2.9405-2.98250.33551110.2696192066
2.9825-3.0270.34591250.2785216874
3.027-3.07430.36381140.2581240481
3.0743-3.12470.36481370.2726253689
3.1247-3.17860.36621390.2731274193
3.1786-3.23630.29021350.2481284197
3.2363-3.29860.30611510.2514285097
3.2986-3.36580.32961650.2383288399
3.3658-3.4390.28821480.2362292399
3.439-3.51890.30251630.2236288099
3.5189-3.60690.30141640.2195288798
3.6069-3.70430.31041700.2207280398
3.7043-3.81320.25481520.2061285297
3.8132-3.93620.23251520.19291599
3.9362-4.07680.23971810.1826285099
4.0768-4.23980.24821570.1772291699
4.2398-4.43250.23631190.1742293999
4.4325-4.66580.19891230.1548292999
4.6658-4.95760.22451180.1569295599
4.9576-5.33950.17761440.15922921100
5.3395-5.87530.20141580.1682947100
5.8753-6.72170.23791750.19122920100
6.7217-8.45460.2261430.1748289497
8.4546-39.10.20221380.1766286695

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