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- PDB-1jtk: Crystal structure of cytidine deaminase from Bacillus subtilis in... -

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Basic information

Entry
Database: PDB / ID: 1jtk
TitleCrystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine
Componentscytidine deaminase
KeywordsHYDROLASE / cytidine deaminase / CDA / pyrimidine salvage pathway
Function / homology
Function and homology information


cytidine deaminase / : / cytidine deaminase 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 ...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
TETRAHYDRODEOXYURIDINE / Cytidine deaminase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJohansson, E. / Mejlhede, N. / Neuhard, J. / Larsen, S.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.
Authors: Johansson, E. / Mejlhede, N. / Neuhard, J. / Larsen, S.
#1: Journal: J.BACTERIOL. / Year: 1999
Title: Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG
Authors: Mejlhede, N. / Atkins, J.F. / Neuhard, J.
History
DepositionAug 21, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytidine deaminase
B: cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3296
Polymers29,7382
Non-polymers5914
Water3,297183
1
A: cytidine deaminase
B: cytidine deaminase
hetero molecules

A: cytidine deaminase
B: cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,65912
Polymers59,4764
Non-polymers1,1838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area11730 Å2
ΔGint-225 kcal/mol
Surface area18140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.086, 66.142, 55.476
Angle α, β, γ (deg.)90.00, 115.92, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe tetrameric cytidine deaminase is constructed from the two chains A and B and the two chains generated by the two-fold axis: -x+1,y,-z+2

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Components

#1: Protein cytidine deaminase


Mass: 14869.015 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: cdd / Plasmid: pSO143 / Production host: Escherichia coli (E. coli) / Strain (production host): JF611 / References: UniProt: P19079, cytidine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-THU / TETRAHYDRODEOXYURIDINE


Mass: 230.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 26% 2-methyl-2,4-pentanediol, 10mM calcium chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.5 mg/mlprotein1drop
25 mMTHU1drop
320 mMTris-HCl1droppH7.6
426 %MPD1reservoir
510 mM1reservoirCaCl2
60.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2001 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 15867 / Num. obs: 15599 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 8.6 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.4
Reflection shellResolution: 2.03→2.08 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.195 / % possible all: 78.7
Reflection
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 20 Å / Num. obs: 15867 / Num. measured all: 214942 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 78.7 % / Rmerge(I) obs: 0.195

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Processing

Software
NameVersionClassification
EPMRphasing
CNS0.9refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTT

1ctt


Resolution: 2.04→19.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1515341.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 777 5 %RANDOM
Rwork0.207 ---
all-15599 --
obs-15599 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.12 Å2 / ksol: 0.360233 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å21.53 Å2
2---0.31 Å20 Å2
3---2.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.04→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 34 183 2193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 122 5.1 %
Rwork0.211 2272 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3THU_PAR.TXTTHU_TOP.TXT
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Highest resolution: 2.04 Å / Lowest resolution: 2.13 Å / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.211 / Rfactor all: 0.213 / Rfactor obs: 0.25

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