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- PDB-5g6d: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 5g6d
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-(((3-(Dimethylamino)benzyl)amino)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 / PROTOPORPHYRIN IX CONTAINING FE / Chem-JHT / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.821 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 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / reflns / reflns_shell
Item: _diffrn_detector.type / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 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 1.6Jan 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)43,0796
Polymers41,7871
Non-polymers1,2925
Water5,441302
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,15812
Polymers83,5742
Non-polymers2,58310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7180 Å2
ΔGint-84.2 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.680, 95.170, 62.230
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 / 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, 307 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-JHT / 7-[[[3-(dimethylamino)phenyl]methylamino]methyl]quinolin-2-amine


Mass: 306.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N4
#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.: 302 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
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: BL12-2 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→37.8 Å / Num. obs: 43528 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 23.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.9
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.882 / % possible all: 96.2

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Processing

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

4lwa


Resolution: 1.821→30.771 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 18.98 / Stereochemistry target values: ML
Details: RAW DATA WAS HIGHLY ANISOTROPIC AND WAS FURTHER SCALED USING THE DIFFRACTION ANISOTROPY SERVER AVAILABLE THROUGH UCLA
RfactorNum. reflection% reflection
Rfree0.1892 1926 5.1 %
Rwork0.1567 --
obs0.1584 37816 86.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→30.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 90 302 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113115
X-RAY DIFFRACTIONf_angle_d1.4644237
X-RAY DIFFRACTIONf_dihedral_angle_d14.2621153
X-RAY DIFFRACTIONf_chiral_restr0.098435
X-RAY DIFFRACTIONf_plane_restr0.006541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8208-1.86630.2398570.1795813X-RAY DIFFRACTION28
1.8663-1.91680.2075720.16911450X-RAY DIFFRACTION50
1.9168-1.97320.20761100.18081890X-RAY DIFFRACTION65
1.9732-2.03690.22321230.18152339X-RAY DIFFRACTION80
2.0369-2.10960.24481320.18782755X-RAY DIFFRACTION94
2.1096-2.19410.2261300.17812953X-RAY DIFFRACTION100
2.1941-2.29390.20751760.16282905X-RAY DIFFRACTION100
2.2939-2.41480.18821770.16372908X-RAY DIFFRACTION100
2.4148-2.5660.18751750.15382913X-RAY DIFFRACTION100
2.566-2.7640.19971510.16062950X-RAY DIFFRACTION100
2.764-3.0420.24531410.16862976X-RAY DIFFRACTION100
3.042-3.48160.16341520.15852972X-RAY DIFFRACTION99
3.4816-4.38450.16251590.13662994X-RAY DIFFRACTION99
4.3845-30.77520.17181710.14443072X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 5.7256 Å / Origin y: 19.729 Å / Origin z: 22.5771 Å
111213212223313233
T0.1499 Å2-0.0116 Å20.0147 Å2-0.1422 Å2-0.0297 Å2--0.1308 Å2
L1.062 °20.1907 °20.1274 °2-1.6939 °2-0.4275 °2--1.1181 °2
S-0.0584 Å °0.1478 Å °0.105 Å °-0.2051 Å °0.0713 Å °-0.0322 Å °-0.113 Å °0.0543 Å °-0.0119 Å °
Refinement TLS groupSelection details: ALL

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