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- PDB-4d3t: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Entry
Database: PDB / ID: 4d3t
TitleStructure of Bacillus subtilis Nitric Oxide Synthase 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: 1.55 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)43,48211
Polymers41,7871
Non-polymers1,69510
Water5,567309
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96522
Polymers83,5742
Non-polymers3,39020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9180 Å2
ΔGint-78.6 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.421, 94.915, 62.859
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-2283-

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Sequence detailsMUTATIONS E25A, E26A, AND 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: 2.87 Å3/Da / Density % sol: 57.15 %
Description: CC ONE HALF FOR FULL DATA SET AT 0.999 CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.601 RMERGE FOR HIGH RESOLUTION SHELL AT 2.151
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: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.55→37.02 Å / Num. obs: 69172 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.57 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 0.7 / % possible all: 92.5

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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 4LWA

4lwa


Resolution: 1.55→37.025 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 3514 5.1 %
Rwork0.1782 --
obs0.1793 68910 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→37.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 114 309 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063133
X-RAY DIFFRACTIONf_angle_d1.2474248
X-RAY DIFFRACTIONf_dihedral_angle_d13.7661161
X-RAY DIFFRACTIONf_chiral_restr0.07437
X-RAY DIFFRACTIONf_plane_restr0.004543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57120.37371320.40742381X-RAY DIFFRACTION90
1.5712-1.59370.3551570.36362535X-RAY DIFFRACTION97
1.5937-1.61750.35251330.32552634X-RAY DIFFRACTION99
1.6175-1.64280.30561430.30992620X-RAY DIFFRACTION99
1.6428-1.66970.29731260.29222606X-RAY DIFFRACTION99
1.6697-1.69850.2691360.26412660X-RAY DIFFRACTION99
1.6985-1.72940.25841410.25062564X-RAY DIFFRACTION98
1.7294-1.76260.30011200.23942613X-RAY DIFFRACTION98
1.7626-1.79860.24941410.242629X-RAY DIFFRACTION99
1.7986-1.83770.2161450.20942605X-RAY DIFFRACTION99
1.8377-1.88050.25141660.20942592X-RAY DIFFRACTION99
1.8805-1.92750.28741390.23812592X-RAY DIFFRACTION98
1.9275-1.97960.22891480.19542614X-RAY DIFFRACTION99
1.9796-2.03780.20051350.17722620X-RAY DIFFRACTION98
2.0378-2.10360.22561260.19732630X-RAY DIFFRACTION97
2.1036-2.17880.19811310.18582596X-RAY DIFFRACTION97
2.1788-2.2660.1741390.18892576X-RAY DIFFRACTION97
2.266-2.36910.1991530.16622625X-RAY DIFFRACTION98
2.3691-2.4940.19411720.16762599X-RAY DIFFRACTION98
2.494-2.65020.1851420.16072626X-RAY DIFFRACTION98
2.6502-2.85480.20881200.17272642X-RAY DIFFRACTION97
2.8548-3.14190.19111310.16952676X-RAY DIFFRACTION99
3.1419-3.59620.1841370.16782677X-RAY DIFFRACTION98
3.5962-4.52960.16581430.14632655X-RAY DIFFRACTION96
4.5296-37.03550.18761580.16072829X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 5.7958 Å / Origin y: 19.5079 Å / Origin z: 23.0066 Å
111213212223313233
T0.2477 Å2-0.0225 Å20.0291 Å2-0.2087 Å2-0.0214 Å2--0.2961 Å2
L0.8413 °20.276 °20.183 °2-1.7011 °2-0.2899 °2--1.0101 °2
S-0.0769 Å °0.1328 Å °0.0685 Å °-0.2657 Å °0.0816 Å °-0.0867 Å °-0.1256 Å °0.0934 Å °-0.001 Å °
Refinement TLS groupSelection details: ALL

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