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- PDB-7f0z: Crystal structure of NsrQ W31A -

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Basic information

Entry
Database: PDB / ID: 7f0z
TitleCrystal structure of NsrQ W31A
ComponentsNsrQ
KeywordsISOMERASE / tetrahydroxanthones / blennolides
Function / homology: / Oxidoreductases / NTF2-like domain superfamily / monooxygenase activity / Monooxygenase nsrQ
Function and homology information
Biological speciesAspergillus novofumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, J. / Mori, T. / Abe, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural Basis for Isomerization Reactions in Fungal Tetrahydroxanthone Biosynthesis and Diversification.
Authors: Yang, J. / Mori, T. / Wei, X. / Matsuda, Y. / Abe, I.
History
DepositionJun 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: NsrQ
B: NsrQ


Theoretical massNumber of molelcules
Total (without water)38,2292
Polymers38,2292
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-17 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.769, 52.150, 61.525
Angle α, β, γ (deg.)90.000, 94.815, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein NsrQ


Mass: 19114.723 Da / Num. of mol.: 2 / Mutation: W31A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus novofumigatus (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I1C3W8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM citrate buffer (pH 5.5), 980 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2→45.61 Å / Num. obs: 19630 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5702 / CC1/2: 0.657 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F0O

7f0o


Resolution: 2→45.61 Å / SU ML: 0.2586 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.9453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 1961 10 %
Rwork0.2033 17643 -
obs0.2086 19604 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.57 Å2
Refinement stepCycle: LAST / Resolution: 2→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 131 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862303
X-RAY DIFFRACTIONf_angle_d0.97473124
X-RAY DIFFRACTIONf_chiral_restr0.055343
X-RAY DIFFRACTIONf_plane_restr0.0082403
X-RAY DIFFRACTIONf_dihedral_angle_d16.6973825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.29451400.24641240X-RAY DIFFRACTION99.93
2.05-2.110.27221530.23071229X-RAY DIFFRACTION98.86
2.11-2.170.29311380.22321264X-RAY DIFFRACTION99.93
2.17-2.240.27441230.22331267X-RAY DIFFRACTION99.78
2.24-2.320.28071550.2161217X-RAY DIFFRACTION99.06
2.32-2.410.35781310.2211279X-RAY DIFFRACTION99.72
2.41-2.520.25781450.2091254X-RAY DIFFRACTION100
2.52-2.650.24631320.20541265X-RAY DIFFRACTION99.86
2.65-2.820.30521520.20221238X-RAY DIFFRACTION99.78
2.82-3.040.27171250.21461294X-RAY DIFFRACTION99.79
3.04-3.340.24011420.1991265X-RAY DIFFRACTION99.65
3.34-3.820.23261470.1841260X-RAY DIFFRACTION99.01
3.83-4.820.221410.17811258X-RAY DIFFRACTION99.43
4.82-45.610.24091370.20821313X-RAY DIFFRACTION98.77

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