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- PDB-4ug6: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4ug6
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)
ComponentsNITRIC OXIDE SYNTHASE OXYGENASE
KeywordsOXIDOREDUCTASE / 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
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / N-PROPANOL / Chem-XFJ / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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

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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)43,3329
Polymers41,7871
Non-polymers1,5458
Water5,350297
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,66418
Polymers83,5742
Non-polymers3,09016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8540 Å2
ΔGint-65.9 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.460, 95.435, 63.350
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-2280-

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 / NITRIC OXIDE SYNTHASE


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 , 7 types, 305 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-XFJ / 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)


Mass: 347.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N5
#6: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.95 Å3/Da / Density % sol: 58.25 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / 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: 1.81→1.85 Å / Num. obs: 45754 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 15.37 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 5.4
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→38.115 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 2352 5.2 %
Rwork0.1915 --
obs0.1936 45658 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→38.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 107 297 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183129
X-RAY DIFFRACTIONf_angle_d1.7064250
X-RAY DIFFRACTIONf_dihedral_angle_d15.4281158
X-RAY DIFFRACTIONf_chiral_restr0.116436
X-RAY DIFFRACTIONf_plane_restr0.007541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.8470.37111460.32252486X-RAY DIFFRACTION100
1.847-1.88710.3191390.29942465X-RAY DIFFRACTION99
1.8871-1.9310.33191420.24852517X-RAY DIFFRACTION100
1.931-1.97930.26641530.22952494X-RAY DIFFRACTION100
1.9793-2.03280.27141350.22142530X-RAY DIFFRACTION100
2.0328-2.09260.25911270.21432516X-RAY DIFFRACTION100
2.0926-2.16020.23551250.19462537X-RAY DIFFRACTION100
2.1602-2.23740.24471150.19632542X-RAY DIFFRACTION100
2.2374-2.32690.23871530.18712522X-RAY DIFFRACTION100
2.3269-2.43280.23711530.1882521X-RAY DIFFRACTION100
2.4328-2.56110.27141590.20042524X-RAY DIFFRACTION100
2.5611-2.72150.26081220.19062571X-RAY DIFFRACTION100
2.7215-2.93150.25531320.19942548X-RAY DIFFRACTION100
2.9315-3.22640.22361210.17292579X-RAY DIFFRACTION100
3.2264-3.6930.20151350.16642611X-RAY DIFFRACTION100
3.693-4.65140.16891480.14772594X-RAY DIFFRACTION100
4.6514-38.12310.19331470.17992749X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.9775 Å / Origin y: 19.9076 Å / Origin z: 23.1376 Å
111213212223313233
T0.0952 Å2-0.0132 Å20.0002 Å2-0.0759 Å2-0.0149 Å2--0.0751 Å2
L0.8803 °20.2106 °20.0822 °2-1.0048 °2-0.1062 °2--0.7752 °2
S-0.042 Å °0.1376 Å °0.051 Å °-0.1512 Å °0.037 Å °-0.0131 Å °-0.0965 Å °0.0637 Å °0.0085 Å °
Refinement TLS groupSelection details: ALL

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