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- PDB-2r9q: Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase f... -

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Basic information

Entry
Database: PDB / ID: 2r9q
TitleCrystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens
Components
  • 2'-deoxycytidine 5'-triphosphate deaminase
  • Synthetic peptide 1Peptide synthesis
  • Synthetic peptide 2Peptide synthesis
KeywordsHYDROLASE / 2'-deoxycytidine 5'-triphosphate deaminase / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


2'-deoxyribonucleotide metabolic process / dCTP deaminase activity
Similarity search - Function
Deoxycytidine triphosphate deaminase, bacterial / 2'-deoxycytidine 5'-triphosphate deaminase (DCD) N-terminal domain / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-deoxycytidine 5'-triphosphate deaminase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Dong, A. / Xu, X. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens.
Authors: Zhang, R. / Dong, A. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE THE AUTHORS FOUND TWO PEPTIDE CHAINS X AND Y BOUND TO MOLECULES B AND C, RESPECTIVELY. ... SEQUENCE THE AUTHORS FOUND TWO PEPTIDE CHAINS X AND Y BOUND TO MOLECULES B AND C, RESPECTIVELY. SINCE THE CHAINS X AND Y ARE UNEXPECTED RESULTS FROM THE CRYSTAL STRUCTURE ANALYSIS, AUTHORS DO NOT KNOW THE EXACT SEQUENCE OF THESE PEPTIDES. THE SEQUENCE OF THE RESIDUES IN THESE TWO CHAINS HAS BEEN ASSIGNED BY THE AUTHORS ACCORDING TO THE ELECTRON DENSITY MAP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2'-deoxycytidine 5'-triphosphate deaminase
B: 2'-deoxycytidine 5'-triphosphate deaminase
C: 2'-deoxycytidine 5'-triphosphate deaminase
D: 2'-deoxycytidine 5'-triphosphate deaminase
X: Synthetic peptide 1
Y: Synthetic peptide 2


Theoretical massNumber of molelcules
Total (without water)163,8196
Polymers163,8196
Non-polymers00
Water11,205622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
MethodPISA
2
A: 2'-deoxycytidine 5'-triphosphate deaminase
C: 2'-deoxycytidine 5'-triphosphate deaminase
X: Synthetic peptide 1


Theoretical massNumber of molelcules
Total (without water)81,8133
Polymers81,8133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
MethodPISA
3
B: 2'-deoxycytidine 5'-triphosphate deaminase
D: 2'-deoxycytidine 5'-triphosphate deaminase
Y: Synthetic peptide 2


Theoretical massNumber of molelcules
Total (without water)82,0063
Polymers82,0063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.693, 129.042, 85.559
Angle α, β, γ (deg.)90.00, 108.75, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological unit of this protein is unknown

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Components

#1: Protein
2'-deoxycytidine 5'-triphosphate deaminase / AGR_C_764p


Mass: 40576.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: dcd, AGR_C_764, Atu0434 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8UI65, UniProt: A9CKA1*PLUS
#2: Protein/peptide Synthetic peptide 1 / Peptide synthesis


Mass: 660.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Protein/peptide Synthetic peptide 2 / Peptide synthesis


Mass: 854.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M CaCl2, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97940, 0.97960
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.2→46.78 Å / Num. all: 73588 / Num. obs: 69099 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 0.8 / Num. unique all: 5433 / % possible all: 53.36

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→46.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.991 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.24
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26949 690 1 %RANDOM
Rwork0.18904 ---
all0.1898 69099 --
obs0.1898 69099 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.38 Å2
2---0.12 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10146 0 0 622 10768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210362
X-RAY DIFFRACTIONr_bond_other_d0.0010.026943
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.97214069
X-RAY DIFFRACTIONr_angle_other_deg1.057316882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21851326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39922.937429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.596151597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0451576
X-RAY DIFFRACTIONr_chiral_restr0.0880.21612
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022137
X-RAY DIFFRACTIONr_nbd_refined0.1890.21858
X-RAY DIFFRACTIONr_nbd_other0.2070.27173
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24616
X-RAY DIFFRACTIONr_nbtor_other0.0870.25886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2530
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1740.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.212
X-RAY DIFFRACTIONr_mcbond_it1.1531.56828
X-RAY DIFFRACTIONr_mcbond_other0.3551.52724
X-RAY DIFFRACTIONr_mcangle_it1.851210653
X-RAY DIFFRACTIONr_scbond_it2.57933913
X-RAY DIFFRACTIONr_scangle_it3.7414.53416
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 39 -
Rwork0.249 2873 -
obs-2912 53.36 %
Refinement TLS params.Method: refined / Origin x: 36.771 Å / Origin y: 52.115 Å / Origin z: 19.641 Å
111213212223313233
T-0.3402 Å2-0.0004 Å20.0268 Å2--0.2869 Å2-0.0082 Å2---0.276 Å2
L0.0222 °2-0.003 °20.0255 °2-0.0427 °2-0.0307 °2--0.0469 °2
S0.0003 Å °-0.0125 Å °-0.0169 Å °-0.0181 Å °0.0094 Å °-0.0043 Å °-0.0167 Å °-0.0045 Å °-0.0097 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 1008 - 99
2X-RAY DIFFRACTION1AA101 - 199100 - 198
3X-RAY DIFFRACTION1AA202 - 300201 - 299
4X-RAY DIFFRACTION1AA301 - 346300 - 345
5X-RAY DIFFRACTION1BB9 - 1008 - 99
6X-RAY DIFFRACTION1BB101 - 199100 - 198
7X-RAY DIFFRACTION1BB202 - 300201 - 299
8X-RAY DIFFRACTION1BB301 - 354300 - 353
9X-RAY DIFFRACTION1CC9 - 1008 - 99
10X-RAY DIFFRACTION1CC101 - 199100 - 198
11X-RAY DIFFRACTION1CC202 - 300201 - 299
12X-RAY DIFFRACTION1CC301 - 346300 - 345
13X-RAY DIFFRACTION1DD9 - 1008 - 99
14X-RAY DIFFRACTION1DD101 - 199100 - 198
15X-RAY DIFFRACTION1DD202 - 300201 - 299
16X-RAY DIFFRACTION1DD301 - 342300 - 341

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