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- PDB-4d3i: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4d3i
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 6,6'-((5-(aminomethyl)-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
Chem-1ET / PROTOPORPHYRIN IX CONTAINING FE / N-PROPANOL / 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: 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

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9916
Polymers41,7871
Non-polymers1,2045
Water4,432246
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,98312
Polymers83,5742
Non-polymers2,40910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6590 Å2
ΔGint-55.7 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.510, 94.940, 63.490
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-2230-

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 , 5 types, 251 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-1ET / 6,6'-{[5-(aminomethyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)


Mass: 375.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Description: CC ONE HALF WAS 0.991 OVERALL AND 0.674 FOR HIGH RESOLUTION SHELL
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: BL7-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2013 / 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: 2.09→44.14 Å / Num. obs: 29389 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 28.91 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.2
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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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: 2.09→44.138 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 1482 5.1 %
Rwork0.1674 --
obs0.17 29338 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→44.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 85 246 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083116
X-RAY DIFFRACTIONf_angle_d1.2384232
X-RAY DIFFRACTIONf_dihedral_angle_d14.0081159
X-RAY DIFFRACTIONf_chiral_restr0.076433
X-RAY DIFFRACTIONf_plane_restr0.004541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.15750.33131170.25882489X-RAY DIFFRACTION100
2.1575-2.23460.30511180.23942499X-RAY DIFFRACTION100
2.2346-2.3240.28031480.24042500X-RAY DIFFRACTION99
2.324-2.42980.23751520.18852492X-RAY DIFFRACTION100
2.4298-2.55790.23571570.17612484X-RAY DIFFRACTION100
2.5579-2.71810.23611180.16812520X-RAY DIFFRACTION100
2.7181-2.9280.27621330.17852528X-RAY DIFFRACTION100
2.928-3.22250.25581190.16922554X-RAY DIFFRACTION100
3.2225-3.68870.21151340.15642550X-RAY DIFFRACTION100
3.6887-4.64650.1691440.13072541X-RAY DIFFRACTION99
4.6465-44.14810.1741420.14812699X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.7322 Å / Origin y: 19.6419 Å / Origin z: 23.1605 Å
111213212223313233
T0.1584 Å2-0.0105 Å20.0173 Å2-0.166 Å2-0.0325 Å2--0.2086 Å2
L0.9622 °20.1591 °20.189 °2-1.9497 °2-0.4809 °2--1.1875 °2
S-0.0537 Å °0.1041 Å °0.0561 Å °-0.2255 Å °0.0567 Å °-0.0522 Å °-0.0619 Å °0.0632 Å °-0.0045 Å °
Refinement TLS groupSelection details: ALL

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