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

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Basic information

Entry
Database: PDB / ID: 4ugj
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)-5-(methyl(2-(methylamino) ethyl)amino)benzonitrile
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-Q1T / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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)43,0045
Polymers41,7871
Non-polymers1,2174
Water4,179232
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,00710
Polymers83,5742
Non-polymers2,4338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6650 Å2
ΔGint-86.2 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.478, 94.663, 62.764
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-2212-

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 , 5 types, 236 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-Q1T / 3-(2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL)-5-(METHYL(2-(METHYLAMINO)ETHYL)AMINO)BENZONITRILE


Mass: 323.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsE25A, E26A, 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: 2.86 Å3/Da / Density % sol: 57 %
Description: CC ONE HALF FOR FULL DATA SET AT 0.999. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.554. RMERGE FOR HIGH RESOLUTION SHELL AT 1.998
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: BL11-1 / Wavelength: 0.97945
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.78→37.03 Å / Num. obs: 46671 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D3T

4d3t


Resolution: 1.78→37.032 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 2388 5.1 %
Rwork0.1779 --
obs0.1795 46583 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→37.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 85 232 3258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113110
X-RAY DIFFRACTIONf_angle_d1.4074231
X-RAY DIFFRACTIONf_dihedral_angle_d14.5621154
X-RAY DIFFRACTIONf_chiral_restr0.092434
X-RAY DIFFRACTIONf_plane_restr0.005541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.81630.36921380.3632524X-RAY DIFFRACTION99
1.8163-1.85580.35581380.32042600X-RAY DIFFRACTION100
1.8558-1.8990.33021480.28012525X-RAY DIFFRACTION100
1.899-1.94650.29471600.24572527X-RAY DIFFRACTION100
1.9465-1.99910.25211420.21922570X-RAY DIFFRACTION100
1.9991-2.05790.27771210.21452589X-RAY DIFFRACTION100
2.0579-2.12430.27151290.20622582X-RAY DIFFRACTION100
2.1243-2.20030.20821150.18682594X-RAY DIFFRACTION100
2.2003-2.28830.22951590.17742578X-RAY DIFFRACTION100
2.2883-2.39250.22131610.17642567X-RAY DIFFRACTION100
2.3925-2.51860.22291650.17542568X-RAY DIFFRACTION100
2.5186-2.67630.20631230.17462613X-RAY DIFFRACTION100
2.6763-2.88290.25081330.1822619X-RAY DIFFRACTION100
2.8829-3.17290.22991230.17862638X-RAY DIFFRACTION100
3.1729-3.63170.19421340.17532645X-RAY DIFFRACTION100
3.6317-4.57420.16111490.14382658X-RAY DIFFRACTION100
4.5742-37.04020.17471500.15662798X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.7188 Å / Origin y: 19.664 Å / Origin z: 22.8608 Å
111213212223313233
T0.265 Å2-0.0105 Å20.0122 Å2-0.258 Å2-0.0219 Å2--0.3149 Å2
L0.772 °20.2155 °20.1334 °2-1.5165 °2-0.3117 °2--0.8676 °2
S-0.0505 Å °0.1322 Å °0.0686 Å °-0.2043 Å °0.0628 Å °-0.0302 Å °-0.0711 Å °0.0646 Å °-0.0083 Å °
Refinement TLS groupSelection details: ALL

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