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- PDB-6xbb: Crystal structure of Streptomyces sviceus SsDesB in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 6xbb
TitleCrystal structure of Streptomyces sviceus SsDesB in complex with NADP+
ComponentsMonooxigenase
KeywordsFLAVOPROTEIN / N-hydroxylase / flavin-dependent monooygenase / desferrioxamine biosynthesis
Function / homology
Function and homology information


L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / nucleotide binding
Similarity search - Function
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.
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-lysine N6-monooxygenase MbtG
Similarity search - Component
Biological speciesStreptomyces sviceus ATCC 29083 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.366 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)398,16724
Polymers385,9358
Non-polymers12,23216
Water21,6361201
1
A: Monooxigenase
B: Monooxigenase
C: Monooxigenase
D: Monooxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,08312
Polymers192,9684
Non-polymers6,1168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29130 Å2
ΔGint-169 kcal/mol
Surface area58270 Å2
MethodPISA
2
E: Monooxigenase
F: Monooxigenase
G: Monooxigenase
H: Monooxigenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,08312
Polymers192,9684
Non-polymers6,1168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29170 Å2
ΔGint-170 kcal/mol
Surface area58330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.125, 153.433, 141.314
Angle α, β, γ (deg.)90.000, 92.440, 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
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1201 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M NaCl, 20% PEG3350, 10 mM sarcosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.366→50 Å / Num. obs: 139487 / % possible obs: 96.3 % / Redundancy: 3.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.089 / Rrim(I) all: 0.103 / Rsym value: 0.053 / Net I/σ(I): 14.2
Reflection shellResolution: 2.366→2.41 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / Num. unique obs: 6996 / CC1/2: 0.729 / CC star: 0.918 / Rpim(I) all: 0.418 / Rrim(I) all: 0.809 / Rsym value: 0.692

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o8p

5o8p


Resolution: 2.366→37.016 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 6786 4.97 %
Rwork0.1894 129711 -
obs0.1919 136497 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.13 Å2 / Biso mean: 35.2461 Å2 / Biso min: 11.09 Å2
Refinement stepCycle: final / Resolution: 2.366→37.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26775 0 808 1201 28784
Biso mean--34.5 33.58 -
Num. residues----3336
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.366-2.39290.30331640.2521302065
2.3929-2.42110.30692000.2457345976
2.4211-2.45060.33592040.2412374783
2.4506-2.48160.29572450.2321407589
2.4816-2.51430.30482210.2375430093
2.5143-2.54870.32151960.2231442595
2.5487-2.58510.2862110.228440196
2.5851-2.62370.2942170.2383444896
2.6237-2.66470.28652240.2264437896
2.6647-2.70830.31312320.2227447296
2.7083-2.7550.29892390.233433396
2.755-2.80510.28462430.2189442096
2.8051-2.8590.28592170.2213439396
2.859-2.91740.29162460.2197442996
2.9174-2.98080.26122260.2136435895
2.9808-3.05010.2731980.2219446196
3.0501-3.12630.30422350.2205443796
3.1263-3.21080.26542210.2161438595
3.2108-3.30520.28962410.212438395
3.3052-3.41180.28092190.2061436995
3.4118-3.53370.24022370.1913442395
3.5337-3.6750.23432370.1838439095
3.675-3.84210.21822470.1742437295
3.8421-4.04450.19642110.1597442295
4.0445-4.29750.19282070.1568446196
4.2975-4.62880.17362610.1442452098
4.6288-5.09350.17572680.1452456499
5.0935-5.82810.18922630.15644612100
5.8281-7.33340.23312280.17814683100
7.3334-370.19362280.1623457197

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