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- PDB-8k6s: Crystal structure of E.coli Cyanase complex with bicarbonate -

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Basic information

Entry
Database: PDB / ID: 8k6s
TitleCrystal structure of E.coli Cyanase complex with bicarbonate
ComponentsCyanate hydratase
KeywordsLYASE / bi-substrate enzyme / native
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
CARBONATE ION / Cyanate hydratase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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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)177,32238
Polymers174,81310
Non-polymers2,50928
Water26,3021460
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.834, 81.050, 81.098
Angle α, β, γ (deg.)70.46, 76.23, 65.48
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.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1460 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.3
Details: 50mM Tris-Cl (pH 7.3), 50 mM potassium phosphate, 2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 197333 / % possible obs: 88.4 % / Redundancy: 3.9 % / CC1/2: 0.97 / CC star: 0.99 / Rmerge(I) obs: 0.18 / Net I/σ(I): 16.88
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 9945 / CC1/2: 0.76 / CC star: 0.93

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MxDCdata collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.86 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1995 1.01 %
Rwork0.1765 --
obs0.1767 196703 88.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 135 1460 13565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612416
X-RAY DIFFRACTIONf_angle_d0.9516791
X-RAY DIFFRACTIONf_dihedral_angle_d6.0511678
X-RAY DIFFRACTIONf_chiral_restr0.0551970
X-RAY DIFFRACTIONf_plane_restr0.0092145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28011430.259614001X-RAY DIFFRACTION89
1.64-1.680.23921460.224514143X-RAY DIFFRACTION90
1.68-1.730.25581430.207513961X-RAY DIFFRACTION89
1.73-1.790.23381390.198913655X-RAY DIFFRACTION86
1.79-1.850.25181360.197513317X-RAY DIFFRACTION85
1.85-1.930.23581470.187114268X-RAY DIFFRACTION91
1.93-2.020.19491450.1714132X-RAY DIFFRACTION90
2.02-2.120.20921410.175513814X-RAY DIFFRACTION88
2.12-2.260.21181370.165213290X-RAY DIFFRACTION84
2.26-2.430.2041460.169314293X-RAY DIFFRACTION91
2.43-2.670.18321440.172414136X-RAY DIFFRACTION90
2.67-3.060.18681410.171313611X-RAY DIFFRACTION87
3.06-3.860.18911470.167814302X-RAY DIFFRACTION91
3.86-48.860.19311400.169413785X-RAY DIFFRACTION88

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