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

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Basic information

Entry
Database: PDB / ID: 4ugu
TitleStructure of Bacillus subtilis Nitric Oxide Synthase in complex with N'-(4-(((2S,4R)-4-(3-((C-thiophen-2-ylcarbonimidoyl)amino)phenoxy) pyrrolidin-2-yl)methoxy)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
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-PQW / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsHolden, J.K. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2015
Title: Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase.
Authors: Holden, J.K. / Dejam, D. / Lewis, M.C. / Huang, H. / Kang, S. / Jing, Q. / Xue, F. / Silverman, R.B. / Poulos, T.L.
History
DepositionMar 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 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 1.4Jan 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)43,2906
Polymers41,7871
Non-polymers1,5035
Water5,765320
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,58012
Polymers83,5742
Non-polymers3,00610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7300 Å2
ΔGint-84.9 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.297, 95.013, 63.083
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-2299-

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 / NITRIC OXIDE SYNTHASE


Mass: 41787.082 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / 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 , 6 types, 325 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-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PQW / N'-[4-[[(2S,4R)-4-[3-[(C-thiophen-2-ylcarbonimidoyl)amino]phenoxy]pyrrolidin-2-yl]methoxy]phenyl]thiophene-2-carboximidamide


Mass: 517.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27N5O2S2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 57.28 %
Description: CC ONE HALF FOR FULL DATA SET AT 0.999. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.926
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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: 0.999999
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.8→49.61 Å / Num. obs: 45321 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 22.57 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1

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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 4D3T

4d3t


Resolution: 1.801→40.887 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 2326 5.1 %
Rwork0.156 --
obs0.1576 45267 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→40.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 103 320 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013130
X-RAY DIFFRACTIONf_angle_d1.4874257
X-RAY DIFFRACTIONf_dihedral_angle_d14.3031164
X-RAY DIFFRACTIONf_chiral_restr0.093437
X-RAY DIFFRACTIONf_plane_restr0.006544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8014-1.83820.29411360.23652464X-RAY DIFFRACTION99
1.8382-1.87810.23991530.20922455X-RAY DIFFRACTION100
1.8781-1.92180.23951370.18232497X-RAY DIFFRACTION100
1.9218-1.96990.20031490.16292497X-RAY DIFFRACTION100
1.9699-2.02320.18921330.15252484X-RAY DIFFRACTION100
2.0232-2.08270.18961230.15192516X-RAY DIFFRACTION100
2.0827-2.14990.19771210.15472510X-RAY DIFFRACTION100
2.1499-2.22670.17111140.15752529X-RAY DIFFRACTION100
2.2267-2.31590.18461530.1472476X-RAY DIFFRACTION100
2.3159-2.42130.19021540.15482515X-RAY DIFFRACTION100
2.4213-2.54890.20781540.15272482X-RAY DIFFRACTION100
2.5489-2.70860.19651210.15482531X-RAY DIFFRACTION100
2.7086-2.91770.21591300.16232547X-RAY DIFFRACTION100
2.9177-3.21120.191220.15652565X-RAY DIFFRACTION100
3.2112-3.67560.17611350.15652574X-RAY DIFFRACTION100
3.6756-4.62980.16131470.13612580X-RAY DIFFRACTION100
4.6298-40.89720.17261440.15732719X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.7207 Å / Origin y: 19.6318 Å / Origin z: 22.988 Å
111213212223313233
T0.1521 Å2-0.0107 Å20.0148 Å2-0.1503 Å2-0.0228 Å2--0.1342 Å2
L0.9203 °20.2082 °20.2004 °2-1.5327 °2-0.3193 °2--1.0257 °2
S-0.0605 Å °0.1445 Å °0.0768 Å °-0.2054 Å °0.0575 Å °-0.0323 Å °-0.1158 Å °0.0744 Å °0.001 Å °
Refinement TLS groupSelection details: ALL

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