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- PDB-11yv: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 11yv
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-((3-(((3-(6-aminopyridin-2-yl)propyl)amino)methyl)phenoxy)methyl)quinolin-2-amine
ComponentsNitric oxide synthase oxygenase
KeywordsOXIDOREDUCTASE / bacterial nitric oxide synthase / inhibitor / nitric oxide
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-V5D / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMurarka, V.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: Anti-MRSA inhibitors targeting bacterial nitric oxide synthase
Authors: Murarka, V.C. / Poulos, T.L.
History
DepositionMar 18, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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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)43,46111
Polymers41,7871
Non-polymers1,67410
Water7,458414
1
A: Nitric oxide synthase oxygenase
hetero molecules

A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92222
Polymers83,5742
Non-polymers3,34820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9580 Å2
ΔGint-68 kcal/mol
Surface area31090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.174, 94.657, 62.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-765-

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 / Mutation: E25A, E26A, E316A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
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, 424 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 60 mM Bis-Tris methane/40 mM citric acid pH 7.6, 20% (v/v) PEG 3350, 1.9% (v/v) 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 26, 2023
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.69→47.33 Å / Num. obs: 55003 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Χ2: 0.93 / Net I/σ(I): 11.7
Reflection shellResolution: 1.69→1.72 Å / Num. unique obs: 2768 / CC1/2: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→44.04 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 498 1.2 %
Rwork0.1629 --
obs0.1633 41363 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 115 414 3478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073242
X-RAY DIFFRACTIONf_angle_d0.8844410
X-RAY DIFFRACTIONf_dihedral_angle_d18.4241227
X-RAY DIFFRACTIONf_chiral_restr0.052445
X-RAY DIFFRACTIONf_plane_restr0.005565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-2.050.21991220.173310041X-RAY DIFFRACTION100
2.05-2.340.21281240.170410138X-RAY DIFFRACTION100
2.34-2.950.23321240.182210158X-RAY DIFFRACTION100
2.95-44.040.17631280.152210528X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.7878 Å / Origin y: 19.6733 Å / Origin z: 22.8963 Å
111213212223313233
T0.2082 Å2-0.0144 Å20.0149 Å2-0.1829 Å2-0.0251 Å2--0.2466 Å2
L1.2322 °20.1228 °20.1165 °2-1.6418 °2-0.1856 °2--1.0061 °2
S-0.0418 Å °0.1794 Å °0.107 Å °-0.2406 Å °0.0558 Å °-0.0467 Å °-0.1259 Å °0.0742 Å °-0.0071 Å °
Refinement TLS groupSelection details: all

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