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- PDB-7n4z: Complex structure of NOS4 with noscapine -

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Basic information

Entry
Database: PDB / ID: 7n4z
TitleComplex structure of NOS4 with noscapine
ComponentsNOS4
KeywordsTRANSCRIPTION / Transcription Factor / Protein Engineering / Specificity / Synthetic Biology
Function / homologynoscapine
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsKim, W. / Zhang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125882 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Using fungible biosensors to evolve improved alkaloid biosyntheses.
Authors: d'Oelsnitz, S. / Kim, W. / Burkholder, N.T. / Javanmardi, K. / Thyer, R. / Zhang, Y. / Alper, H.S. / Ellington, A.D.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NOS4
C: NOS4
B: NOS4
D: NOS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25512
Polymers88,2174
Non-polymers2,0388
Water2,756153
1
A: NOS4
C: NOS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1286
Polymers44,1092
Non-polymers1,0194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-50 kcal/mol
Surface area16770 Å2
MethodPISA
2
B: NOS4
D: NOS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1286
Polymers44,1092
Non-polymers1,0194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-50 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.626, 54.859, 92.640
Angle α, β, γ (deg.)74.140, 81.820, 89.960
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NOS4


Mass: 22054.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-08N / noscapine / (3S)-6,7-dimethoxy-3-[(5R)-4-methoxy-6-methyl-5,6,7,8-tetrahydro-2H-[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one


Mass: 413.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M ammonium sulfate, 0.1 M sodium chloride, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 36886 / % possible obs: 95 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.068 / Rrim(I) all: 0.1 / Χ2: 1.101 / Net I/σ(I): 6.2 / Num. measured all: 66376
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.21-2.251.80.35418160.760.3410.4920.57896.2
2.25-2.291.80.32519100.7830.3120.4510.59895.9
2.29-2.331.70.29318030.8020.2810.4070.67594.6
2.33-2.381.80.25618930.8260.2450.3550.65496.3
2.38-2.431.80.23519080.8830.2250.3260.69297.3
2.43-2.491.80.21218640.880.2020.2930.7596.4
2.49-2.551.70.17619080.9170.1690.2450.82496.7
2.55-2.621.90.17618740.9120.1690.2450.87896.9
2.62-2.71.90.15418300.9360.1470.2140.997.2
2.7-2.781.80.13919370.9410.1320.1921.06796.9
2.78-2.881.80.12218510.9540.1160.1691.06496.3
2.88-31.70.10819060.9520.1030.151.1997.5
3-3.141.80.09318580.9720.0890.1291.26596
3.14-3.31.80.0818470.9720.0760.111.44395.8
3.3-3.511.80.07118460.9840.0680.0981.53395.2
3.51-3.781.90.05517770.9880.0530.0771.4290.7
3.78-4.161.80.05617370.9860.0530.0771.60389
4.16-4.761.80.04716230.990.0440.0651.6185.1
4.76-61.80.04818620.9910.0450.0661.46194.8
6-501.80.05118360.9890.0490.0711.90194.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3VW0

3vw0


Resolution: 2.21→44.07 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 2005 5.44 %
Rwork0.2418 34867 -
obs0.2443 36872 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.04 Å2 / Biso mean: 51.7057 Å2 / Biso min: 19.4 Å2
Refinement stepCycle: final / Resolution: 2.21→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5651 0 120 153 5924
Biso mean--54.17 48.44 -
Num. residues----716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.270.35041410.2862375251691
2.27-2.330.32781400.26952500264095
2.33-2.40.30591530.25662555270896
2.4-2.470.28661430.25532551269497
2.47-2.560.29991410.24442552269397
2.56-2.660.26441460.24282552269897
2.66-2.790.30891460.22942576272297
2.79-2.930.27351430.23362525266897
2.93-3.120.30361500.23512539268997
3.12-3.360.29991440.24392520266496
3.36-3.690.28441380.23872474261293
3.69-4.230.28061310.23492341247289
4.23-5.320.29631370.23272314245188
5.33-44.070.24521520.24682493264595

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