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- PDB-4lwb: Structure of Bacillus subtilis nitric oxide synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4lwb
TitleStructure of Bacillus subtilis nitric oxide synthase in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine
ComponentsNitric oxide synthase oxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE 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 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily ...Nitric oxide synthase, oxygenase subunit / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-QJ8 / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHolden, J.K. / Li, H. / Poulos, T.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and biological studies on bacterial nitric oxide synthase inhibitors.
Authors: Holden, J.K. / Li, H. / Jing, Q. / Kang, S. / Richo, J. / Silverman, R.B. / Poulos, T.L.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3148
Polymers41,7871
Non-polymers1,5277
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nitric oxide synthase oxygenase
hetero molecules

A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,62816
Polymers83,5742
Non-polymers3,05414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7840 Å2
ΔGint-81 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.270, 95.078, 62.739
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-1174-

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 (bacteria)
Strain: 168 / Gene: BSU07630, nos, yflM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34453, EC: 1.14.13.165

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Non-polymers , 6 types, 194 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-QJ8 / 6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine


Mass: 357.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27N5O2
#4: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 60 mM Bis-Tris methane, 40 mM citric acid, 20% PEG3350, 1.9% 1-propanol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 26684 / % possible obs: 99.36 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 34.94 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 17.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1327 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FBZ

2fbz


Resolution: 2.15→43.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.968 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.182 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23292 -5 %RANDOM
Rwork0.18532 ---
obs0.18766 26684 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2---5.94 Å2-0 Å2
3---5.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 105 187 3233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193137
X-RAY DIFFRACTIONr_bond_other_d0.0010.022915
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.9814264
X-RAY DIFFRACTIONr_angle_other_deg0.81836709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6995362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22824.026154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16215522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6541521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213527
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02751
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3323 --
Rwork0.3 1829 -
obs--99.36 %
Refinement TLS params.Method: refined / Origin x: 5.637 Å / Origin y: -20.26 Å / Origin z: -22.282 Å
111213212223313233
T0.106 Å20.0174 Å2-0.0187 Å2-0.1391 Å2-0.004 Å2--0.0085 Å2
L0.9576 °2-0.1549 °2-0.1379 °2-1.8791 °2-0.4227 °2--0.852 °2
S-0.0469 Å °-0.1615 Å °-0.0441 Å °0.2117 Å °0.0423 Å °-0.0803 Å °0.0955 Å °0.0739 Å °0.0046 Å °

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