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

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Basic information

Entry
Database: PDB / ID: 4uqs
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with 3-Bromo-7-Nitroindazole
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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 3-BROMO-7-NITROINDAZOLE / DI(HYDROXYETHYL)ETHER / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Identification of Redox Partners and Development of a Novel Chimeric Bacterial Nitric Oxide Synthase for Structure Activity Analyses.
Authors: Holden, J.K. / Lim, N. / Poulos, T.L.
History
DepositionJun 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: 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)42,7875
Polymers41,7871
Non-polymers1,0004
Water2,486138
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57410
Polymers83,5742
Non-polymers2,0008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7080 Å2
ΔGint-68.1 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.420, 94.530, 63.227
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-2118-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NITRIC OXIDE SYNTHASE OXYGENASE / NITRIC OXIDE SYNTHASE / 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, 142 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-INE / 3-BROMO-7-NITROINDAZOLE


Mass: 242.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4BrN3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.88 Å3/Da / Density % sol: 57.23 % / Description: CC ONE HALF 0.827 RPIM 0.429
Crystal growpH: 7.6
Details: 60 MM BIS-TRIS METHANE/40 MM CITRIC ACID PH 7.6, 15% (VOL/VOL) PEG 3350, 1.9% (VOL/ VOL) 1-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.91837
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.15→49.7 Å / Num. obs: 26866 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.4
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LWA

4lwa


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 17.623 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. N TERMINAL M1 RESIDUE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.28306 1339 5.1 %RANDOM
Rwork0.22863 ---
obs0.2313 24931 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.663 Å2
Baniso -1Baniso -2Baniso -3
1-3.93 Å20 Å20 Å2
2---4.63 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 64 138 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193087
X-RAY DIFFRACTIONr_bond_other_d0.0010.022863
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9684197
X-RAY DIFFRACTIONr_angle_other_deg0.93536592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43224.118153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86715519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0791520
X-RAY DIFFRACTIONr_chiral_restr0.120.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213492
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02731
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_it1.572.0261447
X-RAY DIFFRACTIONr_mcbond_other1.5622.0241446
X-RAY DIFFRACTIONr_mcangle_it2.4033.0311807
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0622.2881640
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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 77 -
Rwork0.342 1841 -
obs--99.12 %
Refinement TLS params.Method: refined / Origin x: 5.334 Å / Origin y: 20.094 Å / Origin z: 22.563 Å
111213212223313233
T0.0879 Å2-0.041 Å20.0296 Å2-0.2173 Å2-0.025 Å2--0.4955 Å2
L0.8847 °20.0289 °20.0846 °2-2.2293 °2-0.431 °2--1.27 °2
S-0.0656 Å °0.0824 Å °0.0676 Å °-0.3101 Å °0.0865 Å °-0.1161 Å °-0.164 Å °0.0903 Å °-0.0209 Å °

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