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- PDB-1k6w: The Structure of Escherichia coli Cytosine Deaminase -

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Basic information

Entry
Database: PDB / ID: 1k6w
TitleThe Structure of Escherichia coli Cytosine Deaminase
ComponentsCytosine Deaminase
KeywordsHYDROLASE / cytosine deaminase / alpha-beta barrel / hexamer / domain swap
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
: / Cytosine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)47,5692
Polymers47,5141
Non-polymers561
Water7,674426
1
A: Cytosine Deaminase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)285,41712
Polymers285,0826
Non-polymers3356
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 area30620 Å2
ΔGint-190 kcal/mol
Surface area81330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.150, 109.150, 240.050
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-904-

HOH

21A-909-

HOH

31A-942-

HOH

41A-984-

HOH

51A-1016-

HOH

DetailsThe biological assembly is a hexamer of three domain swapped dimers generated from 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 / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.011 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2000
RadiationMonochromator: Double cyrstal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.011 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 55446 / Num. obs: 55446 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 42.7
Reflection shellResolution: 1.75→1.86 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 26.8 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 55774 / Num. measured all: 362081
Reflection shell
*PLUS
Lowest resolution: 1.79 Å / % possible obs: 98.6 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 231001.93 / 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
Rfree0.172 2803 5.1 %RANDOM
Rwork0.155 ---
all0.1572 55446 --
obs0.1572 55446 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.1485 Å2 / ksol: 0.4184 e/Å3
Displacement parametersBiso mean: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.59 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 1 426 3752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.187 476 5.2 %
Rwork0.156 8615 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 55695 / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.156 / Rfactor Rfree: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.412
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09
LS refinement shell
*PLUS
Rfactor Rfree: 0.187 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.156

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