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- PDB-1k70: The Structure of Escherichia coli Cytosine Deaminase bound to 4-H... -

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Basic information

Entry
Database: PDB / ID: 1k70
TitleThe Structure of Escherichia coli Cytosine Deaminase bound to 4-Hydroxy-3,4-Dihydro-1H-Pyrimidin-2-one
ComponentsCytosine Deaminase
KeywordsHYDROLASE / cytosine deaminase / alpha-beta barrel / hexamer / conformational change
Function / homology
Function and homology information


cytosine catabolic process / isoguanine deaminase activity / cytosine deaminase / cytosine deaminase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / ferrous iron binding / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
: / Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...: / Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE / Cytosine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsIreton, G.C. / McDermott, G. / Black, M.E. / Stoddard, B.L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The structure of Escherichia coli cytosine deaminase.
Authors: Ireton, G.C. / McDermott, G. / Black, M.E. / Stoddard, B.L.
History
DepositionOct 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosine Deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6843
Polymers47,5141
Non-polymers1702
Water6,612367
1
A: Cytosine Deaminase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)286,10118
Polymers285,0826
Non-polymers1,02012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area30900 Å2
ΔGint-193 kcal/mol
Surface area77040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.500, 109.500, 240.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-922-

HOH

Detailshe biological assembly is a hexamer of three domain swapped dimers generated form the monomer in the asymmetric unit by the operations:-y,x-y,z;y-x,-x,z; y,x,-z;x-y,-y,-z and -x,y-x,z.

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Components

#1: Protein Cytosine Deaminase


Mass: 47513.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25524, cytosine deaminase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HPY / 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE


Mass: 114.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, magnesium chloride, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 7.7 / PH range high: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
211-14 %(w/v)PEG80001reservoir
30.1 MHEPES1reservoirpH7.3-7.7
40.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 2001
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 50003 / Num. obs: 50003 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 12.7 / % possible all: 92.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 51159 / Num. measured all: 331182 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 92.2 % / Mean I/σ(I) obs: 12.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 710238.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2501 5 %RANDOM
Rwork0.176 ---
all0.1782 50003 --
obs0.1782 50003 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0446 Å2 / ksol: 0.402847 e/Å3
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20.25 Å20 Å2
2---0.36 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 9 367 3701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 387 5.1 %
Rwork0.273 7137 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION42HYDROXYP.PARAM2HYDROXYP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.273

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