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- PDB-4d3n: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4d3n
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)-5-((2-(pyridin-2-yl)ethyl)amino)benzonitrile
ComponentsNITRIC OXIDE SYNTHASE OXYGENASE
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR
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, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 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, 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. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / N-PROPANOL / Chem-SK6 / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: J. Med. Chem. / Year: 2015
Title: Structure-based design of bacterial nitric oxide synthase inhibitors.
Authors: Holden, J.K. / Kang, S. / Hollingsworth, S.A. / Li, H. / Lim, N. / Chen, S. / Huang, H. / Xue, F. / Tang, W. / Silverman, R.B. / Poulos, T.L.
History
DepositionOct 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)43,2189
Polymers41,7871
Non-polymers1,4318
Water4,342241
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,43518
Polymers83,5742
Non-polymers2,86116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8330 Å2
ΔGint-43.8 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.700, 93.537, 62.303
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-2223-

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: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / 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 , 5 types, 249 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-SK6 / 3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{[2-(pyridin-2-yl)ethyl]amino}benzonitrile


Mass: 357.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATIONS E25A, E26A AND E316A INTRODUCED

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Description: CC ONE HALF FOR FULL DATASET AT 0.995 CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.915
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: ALS / Beamline: 8.2.1 / Wavelength: 0.999984
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999984 Å / Relative weight: 1
ReflectionResolution: 1.96→49.09 Å / Num. obs: 34237 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 27.16 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.4
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LWA

4lwa


Resolution: 2.13→43.464 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1365 5.1 %
Rwork0.1525 --
obs0.1549 26698 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→43.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 100 241 3282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073124
X-RAY DIFFRACTIONf_angle_d1.2754238
X-RAY DIFFRACTIONf_dihedral_angle_d13.7131158
X-RAY DIFFRACTIONf_chiral_restr0.071435
X-RAY DIFFRACTIONf_plane_restr0.004541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1302-2.20630.22381170.19472505X-RAY DIFFRACTION100
2.2063-2.29460.25281480.18942484X-RAY DIFFRACTION100
2.2946-2.3990.25651480.17232479X-RAY DIFFRACTION100
2.399-2.52550.2171580.1522454X-RAY DIFFRACTION100
2.5255-2.68370.22571210.14922530X-RAY DIFFRACTION100
2.6837-2.89090.22341320.152517X-RAY DIFFRACTION100
2.8909-3.18170.21921190.14992549X-RAY DIFFRACTION100
3.1817-3.64190.17491320.14622555X-RAY DIFFRACTION100
3.6419-4.58770.16931460.12962559X-RAY DIFFRACTION100
4.5877-43.47310.1911440.162701X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.5707 Å / Origin y: 19.3127 Å / Origin z: 22.7389 Å
111213212223313233
T0.1641 Å2-0.0074 Å20.0177 Å2-0.1367 Å2-0.0293 Å2--0.1786 Å2
L1.1187 °20.2916 °20.1638 °2-1.8002 °2-0.4374 °2--1.4164 °2
S-0.0696 Å °0.1449 Å °0.0498 Å °-0.2052 Å °0.0642 Å °-0.0542 Å °-0.076 Å °0.0681 Å °-0.0006 Å °
Refinement TLS groupSelection details: ALL

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