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- PDB-5g66: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 5g66
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 4-methylquinolin-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
PROTOPORPHYRIN IX CONTAINING FE / 4-METHYLQUINOLIN-2-AMINE / DI(HYDROXYETHYL)ETHER / 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: 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 1.2Mar 29, 2017Group: Other
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow / pdbx_database_proc
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 1.5Jan 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)42,9027
Polymers41,7871
Non-polymers1,1146
Water6,071337
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,80314
Polymers83,5742
Non-polymers2,22912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7250 Å2
ΔGint-71.4 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.650, 94.890, 62.240
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-2299-

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 , 6 types, 343 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-M5K / 4-METHYLQUINOLIN-2-AMINE


Mass: 158.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.85 Å3/Da / Density % sol: 56.84 % / Description: NONE
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: SSRL / Beamline: BL7-1 / Wavelength: 1.127
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.76→37.73 Å / Num. obs: 47287 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 21.98 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 3.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LWA

4lwa


Resolution: 1.76→29.57 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 2424 5.1 %
Rwork0.161 --
obs0.1624 47235 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 76 337 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153097
X-RAY DIFFRACTIONf_angle_d1.6244205
X-RAY DIFFRACTIONf_dihedral_angle_d14.1091149
X-RAY DIFFRACTIONf_chiral_restr0.115432
X-RAY DIFFRACTIONf_plane_restr0.008538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.79590.2461380.2222643X-RAY DIFFRACTION100
1.7959-1.8350.23381510.21182631X-RAY DIFFRACTION100
1.835-1.87770.20491580.19062617X-RAY DIFFRACTION100
1.8777-1.92460.19991520.17782627X-RAY DIFFRACTION100
1.9246-1.97660.21071490.1722643X-RAY DIFFRACTION100
1.9766-2.03480.21411370.17152652X-RAY DIFFRACTION100
2.0348-2.10040.20251350.16612652X-RAY DIFFRACTION100
2.1004-2.17550.19361250.16342692X-RAY DIFFRACTION100
2.1755-2.26260.1991460.16172641X-RAY DIFFRACTION100
2.2626-2.36550.1931570.16192643X-RAY DIFFRACTION100
2.3655-2.49020.18041720.15872640X-RAY DIFFRACTION99
2.4902-2.64610.17271400.15292653X-RAY DIFFRACTION99
2.6461-2.85020.23071240.16012663X-RAY DIFFRACTION98
2.8502-3.13680.18131280.16212618X-RAY DIFFRACTION97
3.1368-3.590.17791350.15842587X-RAY DIFFRACTION96
3.59-4.52040.16311280.13832603X-RAY DIFFRACTION94
4.5204-29.57440.19371490.16312606X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 5.627 Å / Origin y: 19.6386 Å / Origin z: 22.6786 Å
111213212223313233
T0.1726 Å2-0.0111 Å20.0163 Å2-0.175 Å2-0.0175 Å2--0.1883 Å2
L1.2767 °20.1494 °20.2016 °2-1.6175 °2-0.3429 °2--0.9254 °2
S-0.0545 Å °0.195 Å °0.1236 Å °-0.1882 Å °0.0669 Å °-0.0305 Å °-0.1089 Å °0.0732 Å °-0.0089 Å °
Refinement TLS groupSelection details: ALL

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