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- PDB-4d3v: Structure of Bacillus subtilis Nitric Oxide Synthase I218V in com... -

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Basic information

Entry
Database: PDB / ID: 4d3v
TitleStructure of Bacillus subtilis Nitric Oxide Synthase I218V in complex with N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]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
PROTOPORPHYRIN IX CONTAINING FE / N-PROPANOL / Chem-RFQ / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors.
Authors: Holden, J.K. / Kang, S. / Hollingsworth, S.A. / Li, H. / Lim, N. / Chen, S. / Huang, H. / Xue, F. / Tang, W. / Silverman, R.B. / Poulos, T.L.
History
DepositionOct 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 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
Revision 2.0Apr 23, 2025Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entry_details
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_entry_details.has_protein_modification

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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)43,62610
Polymers42,0551
Non-polymers1,5719
Water4,900272
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,25320
Polymers84,1112
Non-polymers3,14218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8610 Å2
ΔGint-69.6 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.550, 94.943, 62.133
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-2248-

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: 42055.336 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
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, 281 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RFQ / N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide


Mass: 462.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N4O2S2
#5: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Sequence detailsE25A, E26A, E316A AND I218V INTRODUCED. N TERMINAL RESIDUES GSH ARE CARRYOVER FROM THE CLEAVED HIS TAG.

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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: 2.82 Å3/Da / Density % sol: 56.45 % / Description: NONE
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: ALS / Beamline: 8.2.2 / Wavelength: 0.999746
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999746 Å / Relative weight: 1
ReflectionResolution: 1.88→49.2 Å / Num. obs: 39483 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 30.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

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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 4LWA

4lwa


Resolution: 1.88→49.198 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 2002 5.1 %
Rwork0.1724 --
obs0.1743 39297 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→49.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 106 272 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073125
X-RAY DIFFRACTIONf_angle_d1.3014239
X-RAY DIFFRACTIONf_dihedral_angle_d13.8851157
X-RAY DIFFRACTIONf_chiral_restr0.071435
X-RAY DIFFRACTIONf_plane_restr0.004543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9270.35431480.31942575X-RAY DIFFRACTION99
1.927-1.97910.30321440.27112608X-RAY DIFFRACTION99
1.9791-2.03740.28721360.25262621X-RAY DIFFRACTION99
2.0374-2.10310.28741340.23222642X-RAY DIFFRACTION99
2.1031-2.17830.2261220.20612661X-RAY DIFFRACTION100
2.1783-2.26550.24591500.1972607X-RAY DIFFRACTION99
2.2655-2.36860.22351600.16972641X-RAY DIFFRACTION100
2.3686-2.49350.21311660.16932614X-RAY DIFFRACTION99
2.4935-2.64970.20381410.16512650X-RAY DIFFRACTION99
2.6497-2.85430.24111240.17412672X-RAY DIFFRACTION100
2.8543-3.14150.21891300.17252696X-RAY DIFFRACTION100
3.1415-3.59590.19211390.1682702X-RAY DIFFRACTION100
3.5959-4.530.1681460.13662743X-RAY DIFFRACTION100
4.53-49.21440.18351620.15622863X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.4888 Å / Origin y: 19.4941 Å / Origin z: 22.6268 Å
111213212223313233
T0.2543 Å2-0.0179 Å20.0255 Å2-0.2251 Å2-0.0226 Å2--0.3295 Å2
L1.1778 °2-0.0008 °20.2226 °2-1.6412 °2-0.4225 °2--1.0842 °2
S-0.0418 Å °0.1676 Å °0.1457 Å °-0.1648 Å °0.057 Å °-0.1009 Å °-0.1362 Å °0.125 Å °-0.0072 Å °
Refinement TLS groupSelection details: ALL

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