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- PDB-8k6x: Crystal structure of E.coli Cyanase complex with cyanate and bica... -

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Basic information

Entry
Database: PDB / ID: 8k6x
TitleCrystal structure of E.coli Cyanase complex with cyanate and bicarbonate
ComponentsCyanate hydratase
KeywordsLYASE / bi-substrate enzyme / native / reaction
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 / methanimidate / Cyanate hydratase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)177,35041
Polymers174,81310
Non-polymers2,53831
Water28,3561574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69660 Å2
ΔGint-684 kcal/mol
Surface area47390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.136, 81.137, 81.172
Angle α, β, γ (deg.)70.61, 76.40, 65.34
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.: 21 / 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: Chemical
ChemComp-VQO / methanimidate


Mass: 44.033 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1574 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
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: 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 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 138728 / % possible obs: 88.4 % / Redundancy: 3.8 % / CC1/2: 0.94 / CC star: 0.98 / Rmerge(I) obs: 0.24 / Net I/σ(I): 12.29
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 6748 / CC1/2: 0.56 / CC star: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
MxDCdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.05 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 1998 1.44 %
Rwork0.1669 --
obs0.1675 138602 88.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11970 0 140 1574 13684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812396
X-RAY DIFFRACTIONf_angle_d0.97216766
X-RAY DIFFRACTIONf_dihedral_angle_d5.9931676
X-RAY DIFFRACTIONf_chiral_restr0.0571967
X-RAY DIFFRACTIONf_plane_restr0.0092143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.27471360.22919281X-RAY DIFFRACTION84
1.85-1.90.26991300.20138884X-RAY DIFFRACTION80
1.9-1.950.23521480.18510142X-RAY DIFFRACTION92
1.95-2.020.2141480.173510065X-RAY DIFFRACTION91
2.02-2.090.25951450.17849950X-RAY DIFFRACTION90
2.09-2.170.21431460.17679988X-RAY DIFFRACTION90
2.17-2.270.22021430.16969773X-RAY DIFFRACTION89
2.27-2.390.20741310.17339033X-RAY DIFFRACTION81
2.39-2.540.21681460.17019975X-RAY DIFFRACTION90
2.54-2.730.24221500.179810228X-RAY DIFFRACTION93
2.73-3.010.22721470.170510085X-RAY DIFFRACTION91
3.01-3.450.20561350.15879237X-RAY DIFFRACTION84
3.45-4.340.17651490.139510139X-RAY DIFFRACTION92
4.34-49.050.16811440.15629824X-RAY DIFFRACTION89

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