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

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Basic information

Entry
Database: PDB / ID: 4ugm
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with N,N'-(ethane-1,2-diyldibenzene-3,1-diyl)dithiophene-2-carboximidamide
ComponentsNITRIC OXIDE SYNTHASE OXYGENASE
KeywordsOXIDOREDUCTASE / 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-1QE / 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: 2.09 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)43,1115
Polymers41,7871
Non-polymers1,3244
Water2,666148
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,22210
Polymers83,5742
Non-polymers2,6488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6620 Å2
ΔGint-77.4 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.530, 95.050, 62.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 , 5 types, 152 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-1QE / N,N'-(ethane-1,2-diyldibenzene-3,1-diyl)dithiophene-2-carboximidamide


Mass: 430.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N4S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Description: CC ONE HALF FOR FULL DATASET AT 0.996. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.841
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: BL7-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→49.57 Å / Num. obs: 29294 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

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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: 2.09→40.929 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1481 5.1 %
Rwork0.1906 --
obs0.1928 29239 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→40.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 91 148 3180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083118
X-RAY DIFFRACTIONf_angle_d1.3074242
X-RAY DIFFRACTIONf_dihedral_angle_d14.6151155
X-RAY DIFFRACTIONf_chiral_restr0.073434
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.15750.32371180.25412480X-RAY DIFFRACTION100
2.1575-2.23460.27341180.23432491X-RAY DIFFRACTION100
2.2346-2.3240.2841490.2232497X-RAY DIFFRACTION100
2.324-2.42980.26371470.21812475X-RAY DIFFRACTION100
2.4298-2.55790.25741570.20442441X-RAY DIFFRACTION100
2.5579-2.71810.25061210.20062534X-RAY DIFFRACTION100
2.7181-2.92790.2581320.21592501X-RAY DIFFRACTION100
2.9279-3.22250.28111180.21142546X-RAY DIFFRACTION100
3.2225-3.68850.24561330.1982548X-RAY DIFFRACTION100
3.6885-4.64610.20361450.15462553X-RAY DIFFRACTION100
4.6461-40.93690.18421430.16242692X-RAY DIFFRACTION100

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