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- PDB-6xk4: Nitric Oxide Synthase from Bacillus subtilis in complex with 7-((... -

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Basic information

Entry
Database: PDB / ID: 6xk4
TitleNitric Oxide Synthase from Bacillus subtilis in complex with 7-((3-(((3-(6-aminopyridin-2-yl)propyl)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-V5D / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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)42,9595
Polymers41,7871
Non-polymers1,1724
Water1,78399
1
A: Nitric oxide synthase oxygenase
hetero molecules

A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,91710
Polymers83,5742
Non-polymers2,3438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area6330 Å2
ΔGint-89 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.490, 95.050, 62.740
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-1093-

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, 103 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-V5D / 7-{[3-({[4-(6-aminopyridin-2-yl)butyl]amino}methyl)phenoxy]methyl}quinolin-2-amine


Mass: 427.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N5O / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→37.06 Å / Num. obs: 27561 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 33 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04911 / Rpim(I) all: 0.04911 / Rrim(I) all: 0.06945 / Net I/σ(I): 7.51
Reflection shellResolution: 2.13→2.206 Å / Rmerge(I) obs: 0.3799 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 2689 / CC1/2: 0.822 / Rrim(I) all: 0.5372

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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: 2.13→37.06 Å / SU ML: 0.2831 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 2000 7.26 %
Rwork0.2088 25536 -
obs0.2115 27536 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.35 Å2
Refinement stepCycle: LAST / Resolution: 2.13→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 82 99 3121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393106
X-RAY DIFFRACTIONf_angle_d0.91624221
X-RAY DIFFRACTIONf_chiral_restr0.0461432
X-RAY DIFFRACTIONf_plane_restr0.0036539
X-RAY DIFFRACTIONf_dihedral_angle_d8.8182430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.3311410.30091794X-RAY DIFFRACTION99.74
2.18-2.240.34251390.29251791X-RAY DIFFRACTION99.84
2.24-2.310.30251400.26461783X-RAY DIFFRACTION99.79
2.31-2.380.30411420.25411803X-RAY DIFFRACTION99.85
2.38-2.470.36251390.24131786X-RAY DIFFRACTION99.64
2.47-2.570.28371420.23231809X-RAY DIFFRACTION99.54
2.57-2.680.28751420.23561806X-RAY DIFFRACTION99.64
2.68-2.820.30851410.2421805X-RAY DIFFRACTION99.74
2.83-30.32221430.24651823X-RAY DIFFRACTION99.9
3-3.230.30471420.23061816X-RAY DIFFRACTION99.9
3.23-3.560.25971440.22711837X-RAY DIFFRACTION99.95
3.56-4.070.21461440.1811837X-RAY DIFFRACTION99.7
4.07-5.130.15651460.15011879X-RAY DIFFRACTION99.95
5.13-37.060.18221550.17131967X-RAY DIFFRACTION99.86

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