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- PDB-7f10: Crystal structure of NsrQ M128I in complex with substrate analogue 3 -

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Basic information

Entry
Database: PDB / ID: 7f10
TitleCrystal structure of NsrQ M128I in complex with substrate analogue 3
ComponentsNsrQ
KeywordsISOMERASE / tetrahydroxanthones / blennolides
Function / homology: / Oxidoreductases / NTF2-like domain superfamily / monooxygenase activity / Chem-0BJ / Monooxygenase nsrQ
Function and homology information
Biological speciesAspergillus novofumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Assembly

Deposited unit
A: NsrQ
B: NsrQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7263
Polymers38,4242
Non-polymers3021
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.181, 64.175, 87.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NsrQ


Mass: 19211.818 Da / Num. of mol.: 2 / Mutation: M128I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus novofumigatus (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I1C3W8
#2: Chemical ChemComp-0BJ / methyl 2-[2,6-bis(oxidanyl)phenyl]carbonyl-5-methyl-3-oxidanyl-benzoate


Mass: 302.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES (pH7.5), 20% w/v PEG4000

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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: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.46 Å / Num. obs: 40186 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 22.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2042 / CC1/2: 0.893 / % possible all: 100

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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: 1.65→43.77 Å / SU ML: 0.1835 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 1987 4.95 %
Rwork0.1985 38136 -
obs0.1997 40123 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.39 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 22 307 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762297
X-RAY DIFFRACTIONf_angle_d1.08273136
X-RAY DIFFRACTIONf_chiral_restr0.063340
X-RAY DIFFRACTIONf_plane_restr0.007406
X-RAY DIFFRACTIONf_dihedral_angle_d12.1736304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.30121590.26662688X-RAY DIFFRACTION99.62
1.69-1.740.28541390.23772655X-RAY DIFFRACTION99.71
1.74-1.790.25471150.21832720X-RAY DIFFRACTION99.82
1.79-1.850.2811270.22132704X-RAY DIFFRACTION99.86
1.85-1.910.26591320.23592672X-RAY DIFFRACTION99.93
1.91-1.990.22151470.2122712X-RAY DIFFRACTION99.97
1.99-2.080.22861470.21192693X-RAY DIFFRACTION100
2.08-2.190.25491240.20892719X-RAY DIFFRACTION100
2.19-2.330.22951580.21442697X-RAY DIFFRACTION99.96
2.33-2.50.26141450.21222714X-RAY DIFFRACTION99.93
2.51-2.760.25871390.212723X-RAY DIFFRACTION99.76
2.76-3.160.25071610.20412737X-RAY DIFFRACTION99.97
3.16-3.980.17031420.17382794X-RAY DIFFRACTION99.97
3.98-43.770.17891520.172908X-RAY DIFFRACTION99.9

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