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- PDB-5yy2: Crystal structure of AsqI with Zn -

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Basic information

Entry
Database: PDB / ID: 5yy2
TitleCrystal structure of AsqI with Zn
ComponentsUncharacterized protein AsqI
KeywordsMETAL BINDING PROTEIN / hemocyanin like protein / aspoquinolone biosynthesis / secondary metabolism
Function / homology
Function and homology information


cyclopenase / lyase activity / metal ion binding
Similarity search - Function
Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / 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: 2.91 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7062
Polymers85,6411
Non-polymers651
Water181
1
A: Uncharacterized protein AsqI
hetero molecules

A: Uncharacterized protein AsqI
hetero molecules

A: Uncharacterized protein AsqI
hetero molecules

A: Uncharacterized protein AsqI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,8248
Polymers342,5624
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area12370 Å2
ΔGint-226 kcal/mol
Surface area86960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.582, 114.858, 157.750
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: asqI, AN9228 / Production host: Escherichia coli (E. coli) / References: UniProt: C8VJQ3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, PEG1500, HEPES pH7.5

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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: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.91→19.8 Å / Num. obs: 17162 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.995 / Net I/σ(I): 12.96
Reflection shellResolution: 2.91→3.03 Å / Num. unique obs: 2674 / CC1/2: 0.849

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.91→19.8 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2153 899 5.24 %
Rwork0.197 --
obs0.198 17156 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.91→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 1 1 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144743
X-RAY DIFFRACTIONf_angle_d1.2366446
X-RAY DIFFRACTIONf_dihedral_angle_d15.9541744
X-RAY DIFFRACTIONf_chiral_restr0.065674
X-RAY DIFFRACTIONf_plane_restr0.006838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9103-3.0920.3441360.29582659X-RAY DIFFRACTION100
3.092-3.32970.26931320.26222698X-RAY DIFFRACTION100
3.3297-3.66290.23431590.20852679X-RAY DIFFRACTION100
3.6629-4.18850.19651580.18312669X-RAY DIFFRACTION100
4.1885-5.26080.16551500.15722747X-RAY DIFFRACTION100
5.2608-19.84360.20731640.1762805X-RAY DIFFRACTION100

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