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- PDB-5g6g: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 5g6g
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-((2-((Methylamino)methyl)phenoxy)methyl)quinolin-2-amine
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
5,6,7,8-TETRAHYDROBIOPTERIN / Chem-H8B / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2016
Title: Targeting Bacterial Nitric Oxide Synthase with Aminoquinoline-Based Inhibitors.
Authors: Holden, J.K. / Lewis, M.C. / Cinelli, M.A. / Abdullatif, Z. / Pensa, A.V. / Silverman, R.B. / Poulos, T.L.
History
DepositionJun 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: 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 2.0Feb 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / exptl_crystal_grow / pdbx_database_proc / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_biol / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _entity.pdbx_description / _exptl_crystal_grow.temp / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 10, 2024Group: 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)42,9745
Polymers41,7871
Non-polymers1,1874
Water4,035224
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,94710
Polymers83,5742
Non-polymers2,3738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6630 Å2
ΔGint-80.6 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.810, 94.570, 61.970
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-2204-

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 / 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, 228 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-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-H8B / 7-[[2-(methylaminomethyl)phenoxy]methyl]quinolin-2-amine


Mass: 293.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSURFACE ENTROPY MUTATIONS E25A, E26A AND E316A

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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: 2.83 Å3/Da / Density % sol: 56.59 %
Description: CC ONE HALF FOR HIGH RESOLUTION DATA SHELL AT 0.889. DIFFRACTION HAD STRONG ANISOTROPY AND RAW DATA WAS FURTHER SCALED USING THE DIFFRACTION ANISOTROPY SERVER.
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: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→37.59 Å / Num. obs: 33826 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 24.48 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.1
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 0.9 / % possible all: 99.2

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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: 1.981→37.592 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 23.67 / Stereochemistry target values: ML
Details: RAW DATA HAD STRONG ANISOTROPY AND DATA WAS FURTHER SCALED USING THE DIFFRACTION ANISOTROPY SERVER.
RfactorNum. reflection% reflection
Rfree0.2238 1226 5.1 %
Rwork0.1735 --
obs0.176 24083 71.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.981→37.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 83 224 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113109
X-RAY DIFFRACTIONf_angle_d1.4564230
X-RAY DIFFRACTIONf_dihedral_angle_d14.5211150
X-RAY DIFFRACTIONf_chiral_restr0.086434
X-RAY DIFFRACTIONf_plane_restr0.005540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9809-2.06030.2332400.1986702X-RAY DIFFRACTION20
2.0603-2.1540.2919600.21091302X-RAY DIFFRACTION37
2.154-2.26760.2551010.21641736X-RAY DIFFRACTION50
2.2676-2.40960.2571290.20132184X-RAY DIFFRACTION62
2.4096-2.59560.23441620.18822687X-RAY DIFFRACTION77
2.5956-2.85670.27161630.1863304X-RAY DIFFRACTION93
2.8567-3.26990.22321810.17493589X-RAY DIFFRACTION100
3.2699-4.11890.21151770.15073605X-RAY DIFFRACTION100
4.1189-37.59830.20122130.1693748X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.5184 Å / Origin y: 19.7258 Å / Origin z: 22.3401 Å
111213212223313233
T0.1434 Å2-0.0347 Å20.0024 Å2-0.112 Å2-0.0063 Å2--0.0839 Å2
L1.4459 °20.286 °20.1672 °2-1.8007 °2-0.041 °2--1.0426 °2
S-0.0922 Å °0.2221 Å °0.1599 Å °-0.3168 Å °0.1038 Å °-0.0412 Å °-0.1677 Å °0.0706 Å °-0.0011 Å °
Refinement TLS groupSelection details: ALL

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