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- PDB-6xk5: Nitric Oxide Synthase from Bacillus subtilis in complex with 7-((... -

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Basic information

Entry
Database: PDB / ID: 6xk5
TitleNitric Oxide Synthase from Bacillus subtilis in complex with 7-((3-(((4-(6-aminopyridin-2-yl)butyl)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-V4Y / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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)43,1297
Polymers41,7871
Non-polymers1,3426
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.320, 94.990, 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-1144-

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, 206 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-V4Y / 7-{[3-({[3-(6-aminopyridin-2-yl)propyl]amino}methyl)phenoxy]methyl}quinolin-2-amine


Mass: 413.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N5O / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
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: 1.87→34.12 Å / Num. obs: 37828 / % possible obs: 93.72 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04175 / Rpim(I) all: 0.04175 / Rrim(I) all: 0.05904 / Net I/σ(I): 7.53
Reflection shellResolution: 1.87→1.937 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 3559 / CC1/2: 0.911 / Rpim(I) all: 0.322 / Rrim(I) all: 0.4554

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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: 1.87→34.12 Å / SU ML: 0.2241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 1998 5.34 %
Rwork0.1976 35396 -
obs0.2002 37394 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.19 Å2
Refinement stepCycle: LAST / Resolution: 1.87→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 93 200 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01263115
X-RAY DIFFRACTIONf_angle_d1.39654230
X-RAY DIFFRACTIONf_chiral_restr0.0723434
X-RAY DIFFRACTIONf_plane_restr0.0078539
X-RAY DIFFRACTIONf_dihedral_angle_d12.6994433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.35071340.27872400X-RAY DIFFRACTION91.02
1.92-1.970.30031370.25092418X-RAY DIFFRACTION90.96
1.97-2.030.27191380.23632452X-RAY DIFFRACTION91.71
2.03-2.090.28771370.22222418X-RAY DIFFRACTION91.68
2.09-2.170.2811370.22192444X-RAY DIFFRACTION91.36
2.17-2.250.26091390.21462445X-RAY DIFFRACTION91.63
2.25-2.360.23721400.2182481X-RAY DIFFRACTION92.42
2.36-2.480.22711430.21872528X-RAY DIFFRACTION94.38
2.48-2.640.2861460.2182589X-RAY DIFFRACTION96.85
2.64-2.840.25061480.21582621X-RAY DIFFRACTION96.85
2.84-3.120.26451470.21212589X-RAY DIFFRACTION95.7
3.12-3.580.23391470.19232602X-RAY DIFFRACTION96.09
3.58-4.50.21891500.1582671X-RAY DIFFRACTION96.71
4.5-34.120.21851550.16682738X-RAY DIFFRACTION94.79

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