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- PDB-1ctt: TRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYS... -

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Basic information

Entry
Database: PDB / ID: 1ctt
TitleTRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYSIS BY CYTIDINE DEAMINASE
ComponentsCYTIDINE DEAMINASE
KeywordsHYDROLASE
Function / homology
Function and homology information


pyrimidine nucleoside binding / deoxycytidine catabolic process / cytidine deaminase / cytidine deamination / deoxycytidine deaminase activity / 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 and deoxycytidylate deaminase domain ...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
3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE NUCLEOSIDE / Cytidine deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsXiang, S. / Short, S.A. / Wolfenden, R. / Carter, C.W.
CitationJournal: Biochemistry / Year: 1995
Title: Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase.
Authors: Xiang, S. / Short, S.A. / Wolfenden, R. / Carter Jr., C.W.
History
DepositionFeb 11, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: CYTIDINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8653
Polymers31,5701
Non-polymers2962
Water88349
1
A: CYTIDINE DEAMINASE
hetero molecules

A: CYTIDINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7316
Polymers63,1402
Non-polymers5914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5270 Å2
ΔGint-98 kcal/mol
Surface area19330 Å2
MethodPISA, PQS
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
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 700 SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.00000

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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) / 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-DHZ / 3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE NUCLEOSIDE


Mass: 230.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O5
#4: Water ChemComp-HOH / water / Water


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.19 Å3/Da / Density % sol: 76.29 %
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111-16 mg/mlprotein1drop
214-20 %satammonium sulfate1drop
332-45 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 34000 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.5 %
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. measured all: 118087 / Rmerge(I) obs: 0.0781

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Processing

Software
NameVersionClassification
X-PLOR3model building
TNT5Arefinement
X-PLOR3refinement
R-AXISdata reduction
X-PLOR3phasing
RefinementResolution: 2.2→20 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.19 -
obs0.19 30265
Displacement parametersBiso mean: 33.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 17 49 2286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.4

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