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

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Basic information

Entry
Database: PDB / ID: 4ugh
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with N1-(3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)phenyl)-N1,N2- dimethylethane-1,2-diamine
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-4V4 / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 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

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9795
Polymers41,7871
Non-polymers1,1924
Water5,332296
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,95710
Polymers83,5742
Non-polymers2,3838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6900 Å2
ΔGint-78.8 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.540, 94.790, 62.780
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-2271-

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, 300 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-4V4 / N1-(3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)phenyl)-N1,N2-dimethylethane-1,2-diamine


Mass: 298.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.1 %
Description: CC ONE HALF FOR FULL DATASET AT 0.998. CC ONE HALF FOR HIGH RESOLUTION SET AT 0.761
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: BL9-2 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→37.83 Å / Num. obs: 32454 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 21.13 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.9
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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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 4D3T

4d3t


Resolution: 1.994→37.826 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 1345 5.1 %
Rwork0.1623 --
obs0.1646 26314 78.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.994→37.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 83 296 3320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073108
X-RAY DIFFRACTIONf_angle_d1.2024228
X-RAY DIFFRACTIONf_dihedral_angle_d14.2641153
X-RAY DIFFRACTIONf_chiral_restr0.07434
X-RAY DIFFRACTIONf_plane_restr0.004541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9943-2.06560.2552440.208787X-RAY DIFFRACTION25
2.0656-2.14830.3396700.2031453X-RAY DIFFRACTION46
2.1483-2.24610.24281070.19441948X-RAY DIFFRACTION62
2.2461-2.36450.25531440.18532462X-RAY DIFFRACTION79
2.3645-2.51260.23091900.18322884X-RAY DIFFRACTION93
2.5126-2.70650.21021430.16743094X-RAY DIFFRACTION97
2.7065-2.97880.23851620.17033067X-RAY DIFFRACTION97
2.9788-3.40960.21911480.16273075X-RAY DIFFRACTION96
3.4096-4.29470.17791620.14073072X-RAY DIFFRACTION95
4.2947-37.83290.16511750.14853127X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 5.6113 Å / Origin y: 19.5922 Å / Origin z: 22.9388 Å
111213212223313233
T0.0977 Å2-0.0135 Å20.0077 Å2-0.0928 Å2-0.0148 Å2--0.0762 Å2
L0.5212 °20.1517 °20.0894 °2-1.1242 °2-0.3071 °2--0.5818 °2
S-0.0484 Å °0.061 Å °0.0246 Å °-0.134 Å °0.0662 Å °-0.0219 Å °-0.0299 Å °0.0402 Å °0.0033 Å °
Refinement TLS groupSelection details: ALL

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