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- PDB-4d3j: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4d3j
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-(2,2'-(5-amino-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine)
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
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / N-PROPANOL / Chem-XFN / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 22, 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

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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)43,33510
Polymers41,7871
Non-polymers1,5489
Water6,161342
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,67020
Polymers83,5742
Non-polymers3,09618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8570 Å2
ΔGint-77.1 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.623, 95.008, 62.766
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-2314-

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) / 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 , 7 types, 351 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-XFN / 6,6'-[(5-aminobenzene-1,3-diyl)diethane-2,1-diyl]bis(4-methylpyridin-2-amine)


Mass: 361.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N5
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.88 Å3/Da / Density % sol: 57.24 %
Description: CC ONE HALF FOR FULL DATA SET AT 0.999 CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.591
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: BL9-2 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→37.11 Å / Num. obs: 56580 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.74
Reflection shellResolution: 1.67→37.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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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: 1.67→37.109 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 2880 5.1 %
Rwork0.1648 --
obs0.166 56494 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→37.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 106 342 3388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073137
X-RAY DIFFRACTIONf_angle_d1.1694257
X-RAY DIFFRACTIONf_dihedral_angle_d14.821167
X-RAY DIFFRACTIONf_chiral_restr0.073437
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.69740.44161310.37832527X-RAY DIFFRACTION99
1.6974-1.72670.37681400.34522489X-RAY DIFFRACTION100
1.7267-1.75810.30831150.31662548X-RAY DIFFRACTION100
1.7581-1.79190.29881290.28932536X-RAY DIFFRACTION100
1.7919-1.82840.291450.25612484X-RAY DIFFRACTION100
1.8284-1.86820.2651420.2452521X-RAY DIFFRACTION100
1.8682-1.91170.26421430.20842527X-RAY DIFFRACTION100
1.9117-1.95950.22681520.19762512X-RAY DIFFRACTION100
1.9595-2.01240.1931380.1842537X-RAY DIFFRACTION100
2.0124-2.07170.17961250.17372544X-RAY DIFFRACTION100
2.0717-2.13850.19081280.17062523X-RAY DIFFRACTION100
2.1385-2.21490.19251140.15872561X-RAY DIFFRACTION100
2.2149-2.30360.16711530.1522523X-RAY DIFFRACTION100
2.3036-2.40840.1821560.15612545X-RAY DIFFRACTION100
2.4084-2.53540.17951620.15552529X-RAY DIFFRACTION100
2.5354-2.69420.19041200.15162574X-RAY DIFFRACTION100
2.6942-2.90210.20551370.16132577X-RAY DIFFRACTION100
2.9021-3.1940.16851210.15132595X-RAY DIFFRACTION100
3.194-3.65590.1671350.14862626X-RAY DIFFRACTION100
3.6559-4.60470.14891490.13022600X-RAY DIFFRACTION100
4.6047-37.11850.18291450.15722736X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.8666 Å / Origin y: 19.5919 Å / Origin z: 23.0208 Å
111213212223313233
T0.1373 Å20.0035 Å20.0066 Å2-0.1462 Å2-0.0479 Å2--0.2115 Å2
L1.1352 °20.197 °20.2 °2-1.5785 °2-0.3596 °2--1.0513 °2
S-0.0332 Å °0.1662 Å °-0.0045 Å °-0.176 Å °0.0407 Å °0.0043 Å °-0.0488 Å °0.0365 Å °-0.0075 Å °
Refinement TLS groupSelection details: ALL

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