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- PDB-5yy3: Crystal structure of AsqI -

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Basic information

Entry
Database: PDB / ID: 5yy3
TitleCrystal structure of AsqI
ComponentsUncharacterized protein AsqI
KeywordsMETAL BINDING PROTEIN / hemocyanin like protein / aspoquinolone biosynthesis / secondary metabolism
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Other carbon-carbon lyases / monooxygenase activity / metal ion binding
Similarity search - Function
Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Di-copper centre-containing domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.305 Å
AuthorsHara, K. / Hashimoto, H. / Kishimoto, S. / Watanabe, K.
CitationJournal: Nat Commun / Year: 2018
Title: Enzymatic one-step ring contraction for quinolone biosynthesis.
Authors: Kishimoto, S. / Hara, K. / Hashimoto, H. / Hirayama, Y. / Champagne, P.A. / Houk, K.N. / Tang, Y. / Watanabe, K.
History
DepositionDec 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein AsqI


Theoretical massNumber of molelcules
Total (without water)85,6411
Polymers85,6411
Non-polymers00
Water5,026279
1
A: Uncharacterized protein AsqI

A: Uncharacterized protein AsqI

A: Uncharacterized protein AsqI

A: Uncharacterized protein AsqI


Theoretical massNumber of molelcules
Total (without water)342,5624
Polymers342,5624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12220 Å2
ΔGint-72 kcal/mol
Surface area89380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.082, 117.435, 159.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-152-

CYS

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Components

#1: Protein Uncharacterized protein AsqI / Cyclopenase


Mass: 85640.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ANIA_11193 / Production host: Escherichia coli (E. coli) / References: UniProt: C8VJQ3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Amino acids, Tris/Bichine pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→19.912 Å / Num. obs: 35085 / % possible obs: 98.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 15.22
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 5482 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.305→19.912 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.74
RfactorNum. reflection% reflection
Rfree0.2199 1773 5.05 %
Rwork0.1928 --
obs0.1941 35077 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.305→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 0 279 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094805
X-RAY DIFFRACTIONf_angle_d1.1456532
X-RAY DIFFRACTIONf_dihedral_angle_d14.891768
X-RAY DIFFRACTIONf_chiral_restr0.046681
X-RAY DIFFRACTIONf_plane_restr0.006852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3047-2.36690.28991230.2632452X-RAY DIFFRACTION96
2.3669-2.43640.23951390.24592531X-RAY DIFFRACTION99
2.4364-2.51490.32931370.24382524X-RAY DIFFRACTION99
2.5149-2.60460.25521290.22892548X-RAY DIFFRACTION99
2.6046-2.70870.2441330.21242525X-RAY DIFFRACTION99
2.7087-2.83160.26061300.22072564X-RAY DIFFRACTION99
2.8316-2.98040.24261500.22552509X-RAY DIFFRACTION99
2.9804-3.16650.27431590.21352552X-RAY DIFFRACTION99
3.1665-3.40980.23451500.20322534X-RAY DIFFRACTION99
3.4098-3.75090.22871250.19032588X-RAY DIFFRACTION99
3.7509-4.2890.16811260.16032629X-RAY DIFFRACTION99
4.289-5.38590.1511240.14862632X-RAY DIFFRACTION99
5.3859-19.91250.18991480.17572716X-RAY DIFFRACTION100

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