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- PDB-6xk6: Nitric Oxide Synthase from Bacillus subtilis in complex with 7-((... -

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Basic information

Entry
Database: PDB / ID: 6xk6
TitleNitric Oxide Synthase from Bacillus subtilis in complex with 7-((3-(((2-(pyridin-2-yl)ethyl)amino)methyl)phenoxy)methyl)quinolin-2-amine
ComponentsNitric oxide synthase oxygenase
KeywordsOXIDOREDUCTASE/Inhibitor / Inhibitor / Nitric Oxide Synthase / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


nitric-oxide synthase (flavodoxin) / nitric-oxide synthase activity / nitric oxide biosynthetic process / heme binding / metal ion binding
Similarity search - Function
Nitric oxide synthase, oxygenase subunit / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-V57 / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLewis, M.C. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: To Be Published
Title: Selective Anti-MRSA inhibitors targeting Nitric Oxide Synthase
Authors: Lewis, M.C. / Poulos, T.L.
History
DepositionJun 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0086
Polymers41,7871
Non-polymers1,2215
Water3,297183
1
A: Nitric oxide synthase oxygenase
hetero molecules

A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,01512
Polymers83,5742
Non-polymers2,44110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6040 Å2
ΔGint-86 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.160, 94.330, 61.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1123-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitric oxide synthase oxygenase / NOSoxy-like protein


Mass: 41787.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: nos, yflM, BSU07630 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O34453, nitric-oxide synthase (flavodoxin)

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Non-polymers , 5 types, 188 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-V57 / 7-{[3-({[2-(pyridin-2-yl)ethyl]amino}methyl)phenoxy]methyl}quinolin-2-amine


Mass: 384.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 60 mM BisTris and 40mM citric acid pH 7.6 and 20% vol/vol polyethylene glycol (PEG) 3350, and 1% propanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→37.53 Å / Num. obs: 41333 / % possible obs: 99.27 % / Redundancy: 2 % / Biso Wilson estimate: 23.58 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.03991 / Rpim(I) all: 0.03991 / Rrim(I) all: 0.05645 / Net I/σ(I): 8.26
Reflection shellResolution: 1.84→1.906 Å / Rmerge(I) obs: 0.3732 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 4082 / CC1/2: 0.809 / Rpim(I) all: 0.3732 / Rrim(I) all: 0.5278

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D3J

4d3j


Resolution: 1.84→37.53 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 1998 4.85 %
Rwork0.2013 39202 -
obs0.2028 41200 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.16 Å2
Refinement stepCycle: LAST / Resolution: 1.84→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 85 183 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143096
X-RAY DIFFRACTIONf_angle_d1.42214205
X-RAY DIFFRACTIONf_chiral_restr0.0812432
X-RAY DIFFRACTIONf_plane_restr0.0089536
X-RAY DIFFRACTIONf_dihedral_angle_d12.1617426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.31421420.27992773X-RAY DIFFRACTION99.73
1.89-1.940.35771420.30792754X-RAY DIFFRACTION99.08
1.94-1.990.30361410.24222777X-RAY DIFFRACTION100
1.99-2.060.30471390.24032787X-RAY DIFFRACTION99.8
2.06-2.130.27911430.22912790X-RAY DIFFRACTION99.86
2.13-2.220.22111410.22532761X-RAY DIFFRACTION99.55
2.22-2.320.27211410.23532761X-RAY DIFFRACTION99.62
2.32-2.440.2431430.22062802X-RAY DIFFRACTION99.83
2.44-2.590.3221420.21872798X-RAY DIFFRACTION99.43
2.59-2.790.26591430.21562800X-RAY DIFFRACTION99.29
2.79-3.070.26331430.20292805X-RAY DIFFRACTION98.79
3.07-3.520.25071430.18962793X-RAY DIFFRACTION98.72
3.52-4.430.14931450.15512864X-RAY DIFFRACTION99.14
4.43-37.530.17611500.17262937X-RAY DIFFRACTION97.47

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