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- PDB-4ug7: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4ug7
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 3,5-bis(2-(6-amino-4-methylpyridin-2-yl)ethyl)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, 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
Chem-1EV / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2015
Title: Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase.
Authors: Holden, J.K. / Dejam, D. / Lewis, M.C. / Huang, H. / Kang, S. / Jing, Q. / Xue, F. / Silverman, R.B. / Poulos, T.L.
History
DepositionMar 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
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)43,3288
Polymers41,7871
Non-polymers1,5417
Water5,224290
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,65616
Polymers83,5742
Non-polymers3,08214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8090 Å2
ΔGint-87.2 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.444, 95.046, 62.947
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-2269-

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) / Strain: 168 / 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, 297 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN / Tetrahydrobiopterin


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1EV / 3,5-bis[2-(6-amino-4-methylpyridin-2-yl)ethyl]benzonitrile


Mass: 371.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.88 Å3/Da / Density % sol: 57.28 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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: BL9-2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→49.57 Å / Num. obs: 48479 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 22.58 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.5 / % possible all: 98.9

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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 4D3T
Resolution: 1.76→40.917 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 2487 5.1 %
Rwork0.1643 --
obs0.1655 48431 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→40.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 107 290 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083146
X-RAY DIFFRACTIONf_angle_d1.2834278
X-RAY DIFFRACTIONf_dihedral_angle_d14.2011166
X-RAY DIFFRACTIONf_chiral_restr0.082439
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7596-1.79340.23321270.19022504X-RAY DIFFRACTION99
1.7934-1.830.20161450.17712502X-RAY DIFFRACTION100
1.83-1.86980.19721420.1692518X-RAY DIFFRACTION100
1.8698-1.91330.22061400.16662523X-RAY DIFFRACTION100
1.9133-1.96120.19111560.1582524X-RAY DIFFRACTION100
1.9612-2.01420.17891360.16212521X-RAY DIFFRACTION100
2.0142-2.07350.18341280.16122548X-RAY DIFFRACTION100
2.0735-2.14040.21411240.16492530X-RAY DIFFRACTION100
2.1404-2.21690.16981180.16452577X-RAY DIFFRACTION100
2.2169-2.30560.16571540.16392523X-RAY DIFFRACTION100
2.3056-2.41060.1931540.17312522X-RAY DIFFRACTION100
2.4106-2.53760.21721610.17412546X-RAY DIFFRACTION100
2.5376-2.69660.19861230.1642565X-RAY DIFFRACTION100
2.6966-2.90470.23331330.17562575X-RAY DIFFRACTION100
2.9047-3.1970.18411230.16952593X-RAY DIFFRACTION100
3.197-3.65930.19151320.16122607X-RAY DIFFRACTION99
3.6593-4.60930.16811480.14412579X-RAY DIFFRACTION99
4.6093-40.92760.18091430.17022687X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 5.4987 Å / Origin y: 20.0284 Å / Origin z: 22.5192 Å
111213212223313233
T0.1788 Å2-0.0095 Å20.0156 Å2-0.1659 Å2-0.013 Å2--0.133 Å2
L1.0694 °20.2717 °20.2293 °2-1.4355 °2-0.2632 °2--1.0694 °2
S-0.0589 Å °0.1666 Å °0.1023 Å °-0.2105 Å °0.0474 Å °-0.0207 Å °-0.1334 Å °0.0887 Å °0.0117 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 1:363)

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