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- PDB-2fr6: Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine -

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Basic information

Entry
Database: PDB / ID: 2fr6
TitleCrystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine
ComponentsCytidine deaminase
KeywordsHYDROLASE / CYTIDINE DEAMINASE / ZINC / CYTIDINE / URIDINE / PROTEIN-SUBSTRATE COMPLEX / SUBSTRATE-PRODUCT INTERMEDIATE
Function / homology
Function and homology information


Pyrimidine salvage / negative regulation of nucleotide metabolic process / CMP catabolic process / cytidine deaminase / dCMP catabolic process / cytidine deamination / cellular response to external biotic stimulus / deaminase activity / : / cytidine deaminase activity ...Pyrimidine salvage / negative regulation of nucleotide metabolic process / CMP catabolic process / cytidine deaminase / dCMP catabolic process / cytidine deamination / cellular response to external biotic stimulus / deaminase activity / : / cytidine deaminase activity / UMP salvage / nucleoside binding / response to cycloheximide / Neutrophil degranulation / negative regulation of cell growth / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Cytidine deaminase, homotetrameric / 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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / AMMONIA / URIDINE / Cytidine deaminase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsTeh, A.H.
CitationJournal: Biochemistry / Year: 2006
Title: The 1.48 A Resolution Crystal Structure of the Homotetrameric Cytidine Deaminase from Mouse
Authors: Teh, A.H. / Kimura, M. / Yamamoto, M. / Tanaka, N. / Yamaguchi, I. / Kumasaka, T.
History
DepositionJan 19, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / 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 / _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_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: Cytidine deaminase
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,94214
Polymers64,5944
Non-polymers1,34910
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-224 kcal/mol
Surface area19840 Å2
MethodPISA
2
A: Cytidine deaminase
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules

A: Cytidine deaminase
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,88428
Polymers129,1878
Non-polymers2,69720
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area28310 Å2
ΔGint-486 kcal/mol
Surface area37180 Å2
MethodPISA
3
A: Cytidine deaminase
B: Cytidine deaminase
hetero molecules

A: Cytidine deaminase
B: Cytidine deaminase
hetero molecules

C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules

C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,88428
Polymers129,1878
Non-polymers2,69720
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z+1/21
Buried area16300 Å2
ΔGint-335 kcal/mol
Surface area49190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.199, 92.961, 180.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1005-

SO4

21A-1060-

HOH

DetailsTHE BIOLOGICAL ASSEMBLY IS SIMILAR TO THE TETRAMER CONTAINED IN THE ASYMMETRIC UNIT.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytidine deaminase / Cytidine aminohydrolase


Mass: 16148.411 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-21c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56389, cytidine deaminase

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Non-polymers , 6 types, 368 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N3O5
#5: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#6: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.9M AMMONIUM SULPHATE, 0.1M CITRATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 28, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→33.59 Å / Num. all: 42537 / Num. obs: 42537 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.88 / Net I/σ(I): 11.4 / Scaling rejects: 1478
Reflection shellResolution: 2.07→2.14 Å / % possible obs: 99.9 % / Redundancy: 4.53 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.9 / Num. measured all: 19190 / Num. unique all: 4184 / Num. unique obs: 4184 / Χ2: 1.05 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata scaling
CNS1.1refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FR5

2fr5


Resolution: 2.07→33.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 90351.289 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Due to excessive electron density, NH1 of ARG 68 was refined with unit occupancy for both alternate conformations in the four subunits. Disordered atoms were refined with zero occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2130 5 %RANDOM
Rwork0.188 ---
all-42417 --
obs-42417 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.423 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--4.97 Å20 Å2
3----3.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.07→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 78 358 4691
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.07→2.2 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 369 5.3 %
Rwork0.246 6543 -
obs-6912 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2CYT.paramCYT.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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