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- PDB-1af2: CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH URIDINE -

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Basic information

Entry
Database: PDB / ID: 1af2
TitleCRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH URIDINE
ComponentsCYTIDINE DEAMINASE
KeywordsHYDROLASE / DEAMINASE / PROTON TRANSFER / STRAIN / PRODUCT RELEASE
Function / homology
Function and homology information


pyrimidine nucleoside binding / deoxycytidine catabolic process / cytidine deaminase / : / cytidine deaminase activity / nucleobase-containing small molecule interconversion / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Cytidine deaminase, bacteria / Cytidine deaminase, homodimeric / Cytidine/deoxycytidylate deaminase, zinc-binding domain / Cytidine and deoxycytidylate deaminase zinc-binding region / : / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. ...Cytidine deaminase, bacteria / Cytidine deaminase, homodimeric / Cytidine/deoxycytidylate deaminase, zinc-binding domain / Cytidine and deoxycytidylate deaminase zinc-binding region / : / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Cytidine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXiang, S. / Carter, C.W.
CitationJournal: Biochemistry / Year: 1997
Title: The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization.
Authors: Xiang, S. / Short, S.A. / Wolfenden, R. / Carter Jr., C.W.
History
DepositionMar 20, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 28, 2016Group: Other
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_planes / struct_conn / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTIDINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9593
Polymers31,5701
Non-polymers3902
Water88349
1
A: CYTIDINE DEAMINASE
hetero molecules

A: CYTIDINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9196
Polymers63,1402
Non-polymers7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4150 Å2
ΔGint-31 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.300, 120.300, 78.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CYTIDINE DEAMINASE


Mass: 31569.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABF6, cytidine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 5.187 Å3/Da / Density % sol: 76.289 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114-20 %satammonium sulfate1drop
211-16 mg/mlprotein1drop
320 mMuridine1drop
432-45 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 24137 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.22 / % possible all: 70
Reflection
*PLUS
Num. measured all: 65003
Reflection shell
*PLUS
% possible obs: 70 %

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTU

1ctu


Resolution: 2.3→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2 /
Num. reflection% reflection
obs24137 80 %
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 18 49 2287
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PRO1TOPH19X.PRO
X-RAY DIFFRACTION2PARAM_SX.URD1TOPH_SX.URD
X-RAY DIFFRACTION3PARAMCDA_SX.ZNTOPHCDA.ZN0
X-RAY DIFFRACTION4PARAM_SX.WAT1TOPH_SX.WAT
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg2.5

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