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- PDB-6xk8: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 6xk8
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-((3-((((6-aminopyridin-2-yl)methyl)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 / DI(HYDROXYETHYL)ETHER / N-PROPANOL / Chem-V54 / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)43,2679
Polymers41,7871
Non-polymers1,4808
Water2,090116
1
A: Nitric oxide synthase oxygenase
hetero molecules

A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,53418
Polymers83,5742
Non-polymers2,96016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7680 Å2
ΔGint-82 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.599, 94.499, 61.929
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-1105-

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 , 7 types, 124 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-V54 / 7-{[3-({[(6-aminopyridin-2-yl)methyl]amino}methyl)phenoxy]methyl}quinolin-2-amine


Mass: 385.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N5O / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 56.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystallisation conditions: 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 315 / Detector: CCD / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→37.56 Å / Num. obs: 23021 / % possible obs: 99.78 % / Redundancy: 2 % / Biso Wilson estimate: 34.23 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 19.62
Reflection shellResolution: 2.252→2.333 Å / Rmerge(I) obs: 0.05799 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 2234 / CC1/2: 0.995 / % possible all: 99.55

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Processing

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

4d3j


Resolution: 2.25→37.56 Å / SU ML: 0.1904 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 2000 8.7 %
Rwork0.1822 20984 -
obs0.1855 22984 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.33 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 102 116 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773122
X-RAY DIFFRACTIONf_angle_d1.10724235
X-RAY DIFFRACTIONf_chiral_restr0.0537434
X-RAY DIFFRACTIONf_plane_restr0.0053539
X-RAY DIFFRACTIONf_dihedral_angle_d13.2608436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.2441420.20081488X-RAY DIFFRACTION99.45
2.31-2.370.26071380.20261455X-RAY DIFFRACTION99.94
2.37-2.440.25851410.20021467X-RAY DIFFRACTION99.81
2.44-2.520.27141390.20091466X-RAY DIFFRACTION99.69
2.52-2.610.28261410.19631485X-RAY DIFFRACTION100
2.61-2.710.26431410.20051472X-RAY DIFFRACTION99.81
2.71-2.840.27751430.20271498X-RAY DIFFRACTION99.94
2.84-2.990.24851410.20631485X-RAY DIFFRACTION99.82
2.99-3.170.26011410.19931480X-RAY DIFFRACTION99.88
3.17-3.420.2221430.20021504X-RAY DIFFRACTION99.82
3.42-3.760.20211450.18231511X-RAY DIFFRACTION99.88
3.76-4.310.18561430.16241510X-RAY DIFFRACTION99.82
4.31-5.420.17771470.1561542X-RAY DIFFRACTION99.94
5.42-37.560.19851550.171621X-RAY DIFFRACTION99.83

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