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- PDB-3o7u: Crystal structure of Cytosine Deaminase from Escherichia Coli com... -

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Basic information

Entry
Database: PDB / ID: 3o7u
TitleCrystal structure of Cytosine Deaminase from Escherichia Coli complexed with zinc and phosphono-cytosine
ComponentsCytosine deaminase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / (beta-alpha)8 barrel / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cytosine catabolic process / isoguanine deaminase activity / cytosine deaminase / 5-fluorocytosine deaminase activity / 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 / Alpha-Beta 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
Chem-O7U / DI(HYDROXYETHYL)ETHER / Chem-PXN / Cytosine deaminase / Cytosine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.708 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Hall, R.S. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2011
Title: Three-dimensional structure and catalytic mechanism of Cytosine deaminase.
Authors: Hall, R.S. / Fedorov, A.A. / Xu, C. / Fedorov, E.V. / Almo, S.C. / Raushel, F.M.
History
DepositionJul 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Mar 7, 2012Group: Structure summary
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 4, 2023Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn

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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)49,05613
Polymers47,6451
Non-polymers1,41112
Water4,558253
1
A: Cytosine deaminase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)294,33678
Polymers285,8696
Non-polymers8,46772
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation16_454y-2/3,x+2/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area40090 Å2
ΔGint-102 kcal/mol
Surface area75160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.212, 145.212, 200.609
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-429-

ZN

21A-522-

HOH

31A-524-

HOH

41A-618-

HOH

51A-637-

HOH

61A-647-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytosine deaminase /


Mass: 47644.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: codA / Production host: Escherichia coli (E. coli) / References: UniProt: Q53ZC8, UniProt: P25524*PLUS

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Non-polymers , 6 types, 265 molecules

#2: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-O7U / (2R)-2-amino-2,5-dihydro-1,5,2-diazaphosphinin-6(1H)-one 2-oxide


Mass: 147.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6N3O2P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% Pentaerythritol Propoxylate, 0.05M Hepes, 0.2M Potassium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.708→39.208 Å / Num. all: 86951 / Num. obs: 86951 / % possible obs: 98.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.09 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6W

1k6w


Resolution: 1.708→39.208 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1931 4360 5.01 %
Rwork0.1731 --
obs0.1741 86951 98.94 %
all-86951 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.946 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0616 Å20 Å2-0 Å2
2--2.0616 Å2-0 Å2
3----4.1232 Å2
Refinement stepCycle: LAST / Resolution: 1.708→39.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 86 253 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073489
X-RAY DIFFRACTIONf_angle_d1.0174732
X-RAY DIFFRACTIONf_dihedral_angle_d17.5321288
X-RAY DIFFRACTIONf_chiral_restr0.066524
X-RAY DIFFRACTIONf_plane_restr0.004613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7077-1.72710.3115910.32931972X-RAY DIFFRACTION71
1.7271-1.74740.34241410.30472700X-RAY DIFFRACTION98
1.7474-1.76870.28861580.29322764X-RAY DIFFRACTION100
1.7687-1.79110.3041420.27992737X-RAY DIFFRACTION100
1.7911-1.81470.30551410.26182756X-RAY DIFFRACTION100
1.8147-1.83950.27011550.24592770X-RAY DIFFRACTION100
1.8395-1.86580.30241440.24722710X-RAY DIFFRACTION100
1.8658-1.89360.2531380.2382788X-RAY DIFFRACTION100
1.8936-1.92320.25961610.22052746X-RAY DIFFRACTION100
1.9232-1.95480.19781450.20682767X-RAY DIFFRACTION100
1.9548-1.98850.22071440.20282804X-RAY DIFFRACTION100
1.9885-2.02460.2261550.19332750X-RAY DIFFRACTION100
2.0246-2.06360.17451230.17442800X-RAY DIFFRACTION100
2.0636-2.10570.20291540.17722770X-RAY DIFFRACTION100
2.1057-2.15150.20231570.17572723X-RAY DIFFRACTION100
2.1515-2.20150.18351400.17162794X-RAY DIFFRACTION100
2.2015-2.25660.18241400.16592766X-RAY DIFFRACTION100
2.2566-2.31760.19011590.16192773X-RAY DIFFRACTION100
2.3176-2.38580.17931390.16092783X-RAY DIFFRACTION100
2.3858-2.46270.19341570.16032772X-RAY DIFFRACTION100
2.4627-2.55080.20291610.1582763X-RAY DIFFRACTION100
2.5508-2.65290.17271410.15632766X-RAY DIFFRACTION100
2.6529-2.77360.20431250.16182820X-RAY DIFFRACTION100
2.7736-2.91970.19681530.16172795X-RAY DIFFRACTION100
2.9197-3.10260.18281460.1572787X-RAY DIFFRACTION100
3.1026-3.3420.17881370.1482829X-RAY DIFFRACTION100
3.342-3.67810.15251410.13822802X-RAY DIFFRACTION100
3.6781-4.20980.14891600.13882812X-RAY DIFFRACTION100
4.2098-5.30190.15251510.1382840X-RAY DIFFRACTION100
5.3019-39.21840.17391610.17062932X-RAY DIFFRACTION100

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