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

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Basic information

Entry
Database: PDB / ID: 4ugi
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with N1-(6-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-2-yl)-N1,N2- dimethylethane-1,2-diamine
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 / IMIDAZOLE / N-PROPANOL / Chem-SKO / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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)43,26411
Polymers41,7871
Non-polymers1,47710
Water5,639313
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,52822
Polymers83,5742
Non-polymers2,95420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8770 Å2
ΔGint-57.7 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.440, 95.013, 63.030
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-2291-

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 , 7 types, 323 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SKO / N'-[6-[2-(6-AZANYL-4-METHYL-PYRIDIN-2-YL)ETHYL]PYRIDIN-2-YL]-N,N'-DIMETHYL-ETHANE-1,2-DIAMINE


Mass: 299.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N5
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#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: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


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


Mass: 18.015 Da / Num. of mol.: 313 / 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: 57.32 %
Description: CC ONE HALF FOR FULL DATASET AT 0.998. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.669
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: BL7-1 / Wavelength: 0.999999
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.8→49.61 Å / Num. obs: 45386 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 24.45 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 12.4 / % 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 4D3T

4d3t


Resolution: 1.801→40.906 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 19.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 2330 5.1 %
Rwork0.1683 --
obs0.17 45330 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→40.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 101 313 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073119
X-RAY DIFFRACTIONf_angle_d1.2324228
X-RAY DIFFRACTIONf_dihedral_angle_d13.9321155
X-RAY DIFFRACTIONf_chiral_restr0.076434
X-RAY DIFFRACTIONf_plane_restr0.004541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8008-1.83760.33361350.30082463X-RAY DIFFRACTION99
1.8376-1.87750.30831550.28942467X-RAY DIFFRACTION100
1.8775-1.92120.2971380.2322501X-RAY DIFFRACTION100
1.9212-1.96920.20271480.21682507X-RAY DIFFRACTION100
1.9692-2.02250.2251350.19512479X-RAY DIFFRACTION100
2.0225-2.0820.23561240.19462519X-RAY DIFFRACTION100
2.082-2.14920.21931210.1852515X-RAY DIFFRACTION100
2.1492-2.2260.21611120.16912532X-RAY DIFFRACTION100
2.226-2.31510.20121580.16512485X-RAY DIFFRACTION100
2.3151-2.42050.21531510.16032511X-RAY DIFFRACTION100
2.4205-2.54810.22231580.1582491X-RAY DIFFRACTION100
2.5481-2.70770.20221190.15642541X-RAY DIFFRACTION100
2.7077-2.91670.23251300.16952546X-RAY DIFFRACTION100
2.9167-3.21010.21211230.16722555X-RAY DIFFRACTION100
3.2101-3.67430.17821330.16432594X-RAY DIFFRACTION100
3.6743-4.62830.16351460.13532576X-RAY DIFFRACTION100
4.6283-40.91610.18591440.15662718X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.6676 Å / Origin y: 19.8184 Å / Origin z: 23.0205 Å
111213212223313233
T0.178 Å2-0.0147 Å20.0261 Å2-0.1661 Å2-0.0373 Å2--0.187 Å2
L0.9862 °20.174 °20.2056 °2-1.6654 °2-0.4803 °2--1.1614 °2
S-0.0704 Å °0.1358 Å °0.0759 Å °-0.2047 Å °0.0813 Å °-0.0615 Å °-0.0955 Å °0.0616 Å °-0.0128 Å °
Refinement TLS groupSelection details: ALL

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