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- PDB-6asl: Crystal Structure of Flavin monooxygenase CmoJ (earlier YtnJ) bou... -

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Basic information

Entry
Database: PDB / ID: 6asl
TitleCrystal Structure of Flavin monooxygenase CmoJ (earlier YtnJ) bound with FMN
ComponentsPutative monooxygenase MoxC
KeywordsFLAVOPROTEIN / Flavin monooxygenase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / LUMIFLAVIN / N-acetyl-S-alkylcysteine sulfoxide monooxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBhandari, D.M. / Zhao, B. / Li, P. / Begley, T.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationA-0034 United States
CitationJournal: To Be Published
Title: Flavin mediated Pummerer type rearrangement in cysteine salvage pathway
Authors: Bhandari, D.M. / Krishnamoorthy, K. / Zhao, B. / Li, P. / Begley, T.P.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Putative monooxygenase MoxC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3823
Polymers49,6691
Non-polymers7132
Water3,891216
1
A: Putative monooxygenase MoxC
hetero molecules

A: Putative monooxygenase MoxC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7646
Polymers99,3392
Non-polymers1,4254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8570 Å2
ΔGint-29 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.079, 87.079, 194.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative monooxygenase MoxC


Mass: 49669.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: moxC, ytnJ, BSU29310 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34974
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-LFN / LUMIFLAVIN / 7,8,10-TRIMETHYLBENZO[G]PTERIDINE-2,4(3H,10H)-DIONE / Lumiflavin


Mass: 256.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM HEPES pH 7.5, 200 mM KCl, 29%-33% pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.925 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.925 Å / Relative weight: 1
ReflectionResolution: 1.9→38.943 Å / Num. obs: 59542 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.14
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 1 / % possible all: 99.83

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
PHENIX(1.10.1_2155: 000)phasing
Cootmodel building
iMOSFLM7.2.1data reduction
PHENIX(1.10.1_2155: 000)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YW1

1yw1


Resolution: 1.9→38.94 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.201 1998 3.36 %
Rwork0.172 --
obs0.173 59542 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 50 216 3666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013545
X-RAY DIFFRACTIONf_angle_d0.9524810
X-RAY DIFFRACTIONf_dihedral_angle_d19.1182080
X-RAY DIFFRACTIONf_chiral_restr0.058508
X-RAY DIFFRACTIONf_plane_restr0.007630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9032-1.95080.30631380.27174006X-RAY DIFFRACTION99
1.9508-2.00350.25561400.22734011X-RAY DIFFRACTION100
2.0035-2.06250.21341410.20834046X-RAY DIFFRACTION100
2.0625-2.1290.22771400.19674068X-RAY DIFFRACTION100
2.129-2.20510.23231410.17874054X-RAY DIFFRACTION100
2.2051-2.29340.20211420.17734094X-RAY DIFFRACTION100
2.2934-2.39780.20321410.17294057X-RAY DIFFRACTION100
2.3978-2.52410.20681410.1764060X-RAY DIFFRACTION100
2.5241-2.68230.2121430.17794101X-RAY DIFFRACTION100
2.6823-2.88930.21121420.1844113X-RAY DIFFRACTION100
2.8893-3.17990.19151440.17754125X-RAY DIFFRACTION100
3.1799-3.63980.21511450.1644175X-RAY DIFFRACTION100
3.6398-4.58460.15811460.14664227X-RAY DIFFRACTION100
4.5846-38.9510.21151540.17064407X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7309-0.24970.13171.1444-0.28052.3313-0.0294-0.0923-0.10770.0249-0.0068-0.02830.26730.08820.02820.2543-0.0150.02560.24740.00920.2802-12.80056.3941-38.078
21.12040.0575-0.46291.32930.37761.6007-0.04090.118-0.07930.0321-0.05480.20320.2231-0.41680.16510.308-0.0675-0.02120.35070.01760.3355-28.054512.1191-53.7942
30.6575-0.14210.49031.2982-0.73562.9991-0.0569-0.2382-0.0840.0530.17940.23790.2112-0.4175-0.13230.3379-0.09250.00790.41020.030.3923-31.20110.923-35.1472
42.76670.63171.20961.5096-0.30083.9380.1191-0.22570.19530.4934-0.0390.0139-0.36540.23090.06260.5101-0.08440.08650.34120.050.3804-16.38855.7532-14.8557
53.1511-3.41611.50794.18810.33558.66630.2718-0.74630.08390.62030.07551.1511-0.884-1.5535-0.12590.89190.04760.23090.70170.09510.9485-26.11788.7143-2.9727
61.55761.086-0.06512.8845-0.3154.39060.0551-0.05580.08940.151-0.0172-0.04020.20270.109-0.06570.34070.02710.03630.25580.05640.3326-15.7241-3.8685-19.9543
73.2435-1.0110.65714.802-2.64717.81330.11510.2305-0.2424-0.61050.06060.31591.13050.0293-0.24610.5601-0.06350.03260.2486-0.01590.3936-18.4455-12.8404-39.8546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 126 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 127 THROUGH 205 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 206 THROUGH 257 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 258 THROUGH 318 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 319 THROUGH 345 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 346 THROUGH 402 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 403 THROUGH 432 )

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