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- PDB-8k6g: Crystal structure of E.coli Cyanase -

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Basic information

Entry
Database: PDB / ID: 8k6g
TitleCrystal structure of E.coli Cyanase
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
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)177,21435
Polymers174,81310
Non-polymers2,40225
Water30,8061710
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)78.036, 81.110, 81.099
Angle α, β, γ (deg.)70.48, 76.30, 65.38
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.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1710 / 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: 51.96 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.3
Details: 50mM Tris-Cl (pH 7.3), 50mM potassium phosphate, and 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: 1.5→50 Å / Num. obs: 237786 / % possible obs: 87.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.45 Å2 / CC1/2: 0.97 / CC star: 0.99 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.24
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6 / Num. unique obs: 11829 / CC1/2: 0.75 / CC star: 0.93 / % possible all: 87.6

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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: 1.5→48.95 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 1998 5 %
Rwork0.1706 --
obs0.1707 237512 87.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 150 1715 13835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712437
X-RAY DIFFRACTIONf_angle_d0.96516839
X-RAY DIFFRACTIONf_dihedral_angle_d6.0021680
X-RAY DIFFRACTIONf_chiral_restr0.0581971
X-RAY DIFFRACTIONf_plane_restr0.012136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.25441390.235216431X-RAY DIFFRACTION85
1.54-1.580.23261340.221615779X-RAY DIFFRACTION82
1.58-1.630.24281450.205916975X-RAY DIFFRACTION88
1.63-1.680.20381460.195417245X-RAY DIFFRACTION90
1.68-1.740.2181460.191517136X-RAY DIFFRACTION89
1.74-1.810.23191420.192416804X-RAY DIFFRACTION87
1.81-1.890.22721320.186815592X-RAY DIFFRACTION81
1.89-1.990.19561480.172717451X-RAY DIFFRACTION91
1.99-2.110.20511460.172517265X-RAY DIFFRACTION90
2.11-2.280.20751460.166217105X-RAY DIFFRACTION89
2.28-2.510.17931370.163316222X-RAY DIFFRACTION84
2.51-2.870.20761510.16817694X-RAY DIFFRACTION92
2.87-3.610.14551390.155516400X-RAY DIFFRACTION85
3.61-48.950.16461470.154417415X-RAY DIFFRACTION91

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