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- PDB-4d3u: Structure of Bacillus subtilis Nitric Oxide Synthase H128S in com... -

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Basic information

Entry
Database: PDB / ID: 4d3u
TitleStructure of Bacillus subtilis Nitric Oxide Synthase H128S in complex with N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]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
PROTOPORPHYRIN IX CONTAINING FE / N-PROPANOL / Chem-RFQ / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 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 23, 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)43,4969
Polymers42,0181
Non-polymers1,4788
Water3,045169
1
A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules

A: NITRIC OXIDE SYNTHASE OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,99318
Polymers84,0372
Non-polymers2,95616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8310 Å2
ΔGint-65.6 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.930, 94.730, 62.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 42018.293 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (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 , 6 types, 177 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-RFQ / N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide


Mass: 461.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21N4O2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(S)-N-(3-(1-HYDROXY-2-(3-(THIOPHENE-2-CARBOXIMIDAMIDO)PHENOXY)ETHYL)
Sequence detailsE25A, E26A,E316A AND H128S INTRODUCED. N TERIMINAL GSH RESIDUES ARE FROM THE CLEAVED HIS TAG

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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: 2.83 Å3/Da / Density % sol: 56.53 % / Description: NONE
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: BL11-1 / Wavelength: 0.97891
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.98→37.65 Å / Num. obs: 33624 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 36.44 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.1
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1 / % possible all: 99.2

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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: 1.981→29.417 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 1341 5.1 %
Rwork0.1662 --
obs0.1683 26173 77.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.981→29.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 100 169 3206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083116
X-RAY DIFFRACTIONf_angle_d1.3244228
X-RAY DIFFRACTIONf_dihedral_angle_d14.4571155
X-RAY DIFFRACTIONf_chiral_restr0.073434
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.981-2.05180.2432400.2024710X-RAY DIFFRACTION22
2.0518-2.13390.287640.21621339X-RAY DIFFRACTION42
2.1339-2.2310.2589890.2081791X-RAY DIFFRACTION57
2.231-2.34850.24881420.21752199X-RAY DIFFRACTION70
2.3485-2.49560.23561760.20992695X-RAY DIFFRACTION85
2.4956-2.68820.24951570.21383158X-RAY DIFFRACTION99
2.6882-2.95850.2811670.19483166X-RAY DIFFRACTION99
2.9585-3.3860.22561540.17933236X-RAY DIFFRACTION99
3.386-4.2640.1861690.1433208X-RAY DIFFRACTION99
4.264-29.42010.16611830.13483330X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 5.5875 Å / Origin y: 19.6463 Å / Origin z: 22.3769 Å
111213212223313233
T0.2625 Å2-0.0393 Å20.0239 Å2-0.2344 Å2-0.0426 Å2--0.2642 Å2
L1.3839 °20.2523 °20.213 °2-2.1438 °2-0.3838 °2--1.32 °2
S-0.113 Å °0.1898 Å °0.1504 Å °-0.3313 Å °0.1425 Å °-0.0598 Å °-0.1676 Å °0.1042 Å °-0.0227 Å °
Refinement TLS groupSelection details: ALL

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