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- PDB-7f0o: Crystal structure of selenomethionine-labeled isomerase NsrQ -

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Basic information

Entry
Database: PDB / ID: 7f0o
TitleCrystal structure of selenomethionine-labeled isomerase NsrQ
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 / SAD / Resolution: 2.2 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 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NsrQ
B: NsrQ


Theoretical massNumber of molelcules
Total (without water)39,1162
Polymers39,1162
Non-polymers00
Water1,838102
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 area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.719, 52.201, 61.196
Angle α, β, γ (deg.)90.000, 94.777, 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: 19558.121 Da / Num. of mol.: 2
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.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM citrate buffer (pH5.5), 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: 1.1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.56 Å / Num. obs: 14685 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 23.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Net I/σ(I): 20.3
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 7 / Num. unique obs: 1264 / CC1/2: 0.97 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→45.56 Å / SU ML: 0.2351 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.3158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 1474 10.05 %
Rwork0.1916 13189 -
obs0.1979 14663 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 0 102 2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252404
X-RAY DIFFRACTIONf_angle_d0.64713268
X-RAY DIFFRACTIONf_chiral_restr0.044353
X-RAY DIFFRACTIONf_plane_restr0.0047422
X-RAY DIFFRACTIONf_dihedral_angle_d5.0225305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.29561390.21971184X-RAY DIFFRACTION99.1
2.28-2.360.31851270.20411187X-RAY DIFFRACTION100
2.36-2.450.29511270.20131199X-RAY DIFFRACTION100
2.45-2.560.2851420.20921184X-RAY DIFFRACTION100
2.56-2.70.30751300.20221189X-RAY DIFFRACTION100
2.7-2.870.29381370.20261199X-RAY DIFFRACTION100
2.87-3.090.2891340.21551209X-RAY DIFFRACTION99.93
3.09-3.40.23211310.19571182X-RAY DIFFRACTION99.92
3.4-3.890.26181390.18341203X-RAY DIFFRACTION100
3.89-4.90.21081390.16071200X-RAY DIFFRACTION99.78
4.9-45.560.20671290.18651253X-RAY DIFFRACTION99.35

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