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

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Basic information

Entry
Database: PDB / ID: 4ugx
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with N-(3-((ethyl(2-(3-fluorophenyl)ethyl)amino)methyl)phenyl)thiophene-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-5H4 / 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: 1.86 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 1.4Jan 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

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2467
Polymers41,7871
Non-polymers1,4596
Water4,738263
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,49214
Polymers83,5742
Non-polymers2,91812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7460 Å2
ΔGint-84 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.593, 94.927, 62.847
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-2242-

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, 269 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-5H4 / N-[3-({ethyl[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide


Mass: 381.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24FN3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Description: CC ONE HALF FOR FULL DATA SET AT 0.997. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.545
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 315r / Detector: CCD / Date: Mar 29, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→37.88 Å / Num. obs: 40955 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 25.38 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.3 / % possible all: 98.5

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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: 1.86→37.875 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 2111 5.2 %
Rwork0.1634 --
obs0.1652 40897 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→37.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 100 263 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123136
X-RAY DIFFRACTIONf_angle_d1.4984263
X-RAY DIFFRACTIONf_dihedral_angle_d14.4771166
X-RAY DIFFRACTIONf_chiral_restr0.09438
X-RAY DIFFRACTIONf_plane_restr0.006545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8601-1.90330.33171510.30292484X-RAY DIFFRACTION98
1.9033-1.95090.34341580.26392506X-RAY DIFFRACTION99
1.9509-2.00370.23881440.22812530X-RAY DIFFRACTION99
2.0037-2.06260.23291190.20872565X-RAY DIFFRACTION99
2.0626-2.12920.26591290.2072557X-RAY DIFFRACTION99
2.1292-2.20530.19931140.18212549X-RAY DIFFRACTION99
2.2053-2.29360.21821580.16932572X-RAY DIFFRACTION99
2.2936-2.39790.20861590.16362540X-RAY DIFFRACTION99
2.3979-2.52430.21181640.15532557X-RAY DIFFRACTION99
2.5243-2.68250.18421230.15532596X-RAY DIFFRACTION100
2.6825-2.88950.23191330.15382605X-RAY DIFFRACTION100
2.8895-3.18020.20451250.15452636X-RAY DIFFRACTION100
3.1802-3.640.16681350.14872639X-RAY DIFFRACTION100
3.64-4.58480.15651480.13062655X-RAY DIFFRACTION100
4.5848-37.88330.1791510.15642795X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.6864 Å / Origin y: 19.7103 Å / Origin z: 22.8147 Å
111213212223313233
T0.216 Å2-0.0199 Å20.0168 Å2-0.2083 Å2-0.0232 Å2--0.2239 Å2
L0.8751 °20.2079 °20.1476 °2-1.5764 °2-0.2123 °2--1.0642 °2
S-0.0655 Å °0.129 Å °0.0837 Å °-0.2103 Å °0.0733 Å °-0.0705 Å °-0.1387 Å °0.0768 Å °-0.0055 Å °
Refinement TLS groupSelection details: ALL

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