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- PDB-5g6o: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 5g6o
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with two molecules of 7-((4-(Dimethylamino)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
Chem-8VJ / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.719 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 1.3Feb 6, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / struct_biol
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _exptl_crystal_grow.temp
Revision 1.4Jan 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)43,1466
Polymers41,7871
Non-polymers1,3595
Water4,900272
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,29212
Polymers83,5742
Non-polymers2,71810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6230 Å2
ΔGint-88.2 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.747, 94.820, 62.183
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-2248-

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, 277 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-8VJ / 7-[[4-[(dimethylamino)methyl]phenoxy]methyl]quinolin-2-amine


Mass: 307.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSURFACE ENTROPY MUTANTS 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: 2.85 Å3/Da / Density % sol: 56.82 % / Description: CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.654
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: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 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: 1.72→37.7 Å / Num. obs: 51182 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 23.43 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 0.8 / % possible all: 96.5

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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: 1.719→37.702 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2537 5.1 %
Rwork0.1865 --
obs0.1884 49751 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.719→37.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 96 272 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163122
X-RAY DIFFRACTIONf_angle_d1.6784245
X-RAY DIFFRACTIONf_dihedral_angle_d14.4791151
X-RAY DIFFRACTIONf_chiral_restr0.114434
X-RAY DIFFRACTIONf_plane_restr0.008541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7193-1.75240.38371190.36162547X-RAY DIFFRACTION96
1.7524-1.78810.3291320.29622637X-RAY DIFFRACTION98
1.7881-1.8270.28621440.27692631X-RAY DIFFRACTION98
1.827-1.86950.32451600.26822572X-RAY DIFFRACTION98
1.8695-1.91630.36991430.32422540X-RAY DIFFRACTION95
1.9163-1.96810.33311490.2782547X-RAY DIFFRACTION95
1.9681-2.0260.25911410.21592650X-RAY DIFFRACTION99
2.026-2.09140.26251340.23482649X-RAY DIFFRACTION98
2.0914-2.16610.24041300.20712644X-RAY DIFFRACTION98
2.1661-2.25280.27661330.23692552X-RAY DIFFRACTION94
2.2528-2.35540.25811530.2092505X-RAY DIFFRACTION93
2.3554-2.47950.24731660.18512557X-RAY DIFFRACTION95
2.4795-2.63480.20641430.17792578X-RAY DIFFRACTION95
2.6348-2.83820.2321160.17662661X-RAY DIFFRACTION96
2.8382-3.12370.23381290.17362652X-RAY DIFFRACTION97
3.1237-3.57540.19471370.16272688X-RAY DIFFRACTION98
3.5754-4.50340.17331480.13682764X-RAY DIFFRACTION99
4.5034-37.7110.17531600.15362840X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 5.6323 Å / Origin y: 19.6275 Å / Origin z: 22.6227 Å
111213212223313233
T0.2066 Å2-0.016 Å20.0182 Å2-0.1925 Å2-0.0296 Å2--0.2003 Å2
L1.4672 °20.1151 °20.2298 °2-1.8705 °2-0.3442 °2--1.1434 °2
S-0.0549 Å °0.1766 Å °0.1111 Å °-0.2323 Å °0.0684 Å °-0.0495 Å °-0.1137 Å °0.0966 Å °-0.0105 Å °
Refinement TLS groupSelection details: ALL

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