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- PDB-4lwa: Structure of Bacillus subtilis nitric oxide synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4lwa
TitleStructure of Bacillus subtilis nitric oxide synthase in complex with ((2S, 3S)-1,3-bis((6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridin-2-yl)methoxy)-2-aminobutane
ComponentsNitric oxide synthase oxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / Chem-Q13 / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsHolden, J.K. / Li, H. / Poulos, T.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and biological studies on bacterial nitric oxide synthase inhibitors.
Authors: Holden, J.K. / Li, H. / Jing, Q. / Kang, S. / Richo, J. / Silverman, R.B. / Poulos, T.L.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)43,2459
Polymers41,7871
Non-polymers1,4588
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nitric oxide synthase oxygenase
hetero molecules

A: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,49018
Polymers83,5742
Non-polymers2,91616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8050 Å2
ΔGint-97 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.648, 95.029, 63.031
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-1212-

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: E25A, E26A, E316A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU07630, nos, yflM / 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 , 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-Q13 / 6,6'-{[(2S,3S)-2-aminobutane-1,3-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)


Mass: 345.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27N5O2
#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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
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: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 30635 / % possible obs: 99.93 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 29.18 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 26.5
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FBZ

2fbz


Resolution: 2.06→49.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.047 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.142 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.20148 -5 %RANDOM
Rwork0.16466 ---
obs0.16648 30635 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.655 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å2-0 Å2
2---2.81 Å20 Å2
3---4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.06→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 99 243 3283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193118
X-RAY DIFFRACTIONr_bond_other_d0.0010.022907
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.9774232
X-RAY DIFFRACTIONr_angle_other_deg0.82136689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90924.118153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7031520
X-RAY DIFFRACTIONr_chiral_restr0.10.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213501
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 112 -
Rwork0.195 2127 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 5.827 Å / Origin y: 20.28 Å / Origin z: 22.443 Å
111213212223313233
T0.1614 Å2-0.0083 Å2-0.0015 Å2-0.1536 Å2-0.0032 Å2--0.0089 Å2
L0.9994 °20.3246 °20.1003 °2-1.6131 °2-0.3454 °2--0.9812 °2
S-0.0813 Å °0.1593 Å °0.0674 Å °-0.1597 Å °0.0479 Å °-0.0393 Å °-0.099 Å °0.0622 Å °0.0334 Å °

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