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- PDB-1zab: Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-De... -

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Basic information

Entry
Database: PDB / ID: 1zab
TitleCrystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine
ComponentsCytidine deaminase
KeywordsHYDROLASE / mouse / cytidine deaminase / zinc / 3-deazauridine / substrate dissociation
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
Chem-URD / Cytidine deaminase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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
DepositionApr 6, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)65,92413
Polymers64,5944
Non-polymers1,3319
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-240 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)131,84826
Polymers129,1878
Non-polymers2,66118
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area28410 Å2
ΔGint-498 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.237, 92.361, 180.531
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

DetailsThe biological assembly is similar to the tetramer contained in the asymmetric unit

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Components

#1: Protein
Cytidine deaminase


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P56389, cytidine deaminase
#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-URD / 1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE / 3-DEAZAURIDINE


Type: RNA linking / Mass: 243.213 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.7 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Ammonium sulphate, citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 23, 2004
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→48.56 Å / Num. all: 28544 / Num. obs: 28544 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.21 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.8
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 5.28 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2834 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BBSdata reduction
CrystalClear(MSC/RIGAKU)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FR5

2fr5


Resolution: 2.36→48.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 91083.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Disordered atoms were refined with zero occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1368 4.9 %RANDOM
Rwork0.176 ---
obs0.178 28184 98 %-
all-28184 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.5162 Å2 / ksol: 0.37304 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--6.01 Å20 Å2
3----5.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.36→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 77 309 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.36→2.51 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 204 4.4 %
Rwork0.204 4393 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4URD.paramURD.top

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