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- PDB-8k6u: Serial Femtosecond X-ray structure of E.coli Cyanase with un-mode... -

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Basic information

Entry
Database: PDB / ID: 8k6u
TitleSerial Femtosecond X-ray structure of E.coli Cyanase with un-modeled density at active site
ComponentsCyanate hydratase
KeywordsLYASE / bi-substrate enzyme / enzyme reaction / room temperature
Function / homology
Function and homology information


cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function
: / Cyanate hydratase, N-terminal / Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, J. / Nam, K.H. / Cho, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural mechanism of Escherichia coli cyanase.
Authors: Kim, J. / Kim, Y. / Park, J. / Nam, K.H. / Cho, Y.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase
F: Cyanate hydratase
G: Cyanate hydratase
H: Cyanate hydratase
I: Cyanate hydratase
J: Cyanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,29315
Polymers174,81310
Non-polymers4805
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67190 Å2
ΔGint-511 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.400, 80.900, 82.300
Angle α, β, γ (deg.)70.00, 72.00, 65.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cyanate hydratase / Cyanase / Cyanate hydrolase / Cyanate lyase


Mass: 17481.266 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cynS, cnt, b0340, JW0331 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00816, cyanase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.3
Details: 50mM Tris-Cl (pH 7.3), 50 mM potassium phosphate, and 2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.305 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 1.9→75.9 Å / Num. obs: 266307 / % possible obs: 100 % / Redundancy: 295.4 % / CC1/2: 0.96 / CC star: 0.99 / R split: 0.18 / Net I/σ(I): 4.54
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 1.41 / Num. unique obs: 18842 / CC1/2: 0.35 / R split: 0.83

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MxDCdata collection
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→57.13 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1893 7.1 %
Rwork0.1719 --
obs0.1721 266307 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→57.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 25 603 12598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812294
X-RAY DIFFRACTIONf_angle_d1.05716620
X-RAY DIFFRACTIONf_dihedral_angle_d6.2521672
X-RAY DIFFRACTIONf_chiral_restr0.061964
X-RAY DIFFRACTIONf_plane_restr0.0082131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31141370.313918842X-RAY DIFFRACTION100
1.95-20.31191380.267518874X-RAY DIFFRACTION100
2-2.060.28921300.254319028X-RAY DIFFRACTION100
2.06-2.130.25151360.230918880X-RAY DIFFRACTION100
2.13-2.20.25271400.222518878X-RAY DIFFRACTION100
2.2-2.290.24321260.196918787X-RAY DIFFRACTION100
2.29-2.390.2091440.199518878X-RAY DIFFRACTION100
2.39-2.520.20771300.183118952X-RAY DIFFRACTION100
2.52-2.680.24531320.189918886X-RAY DIFFRACTION100
2.68-2.880.23121380.168718892X-RAY DIFFRACTION100
2.88-3.170.21081320.171318888X-RAY DIFFRACTION100
3.17-3.630.14241340.145818896X-RAY DIFFRACTION100
3.63-4.580.16091400.132618872X-RAY DIFFRACTION100
4.58-57.130.17241360.144118861X-RAY DIFFRACTION100

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