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- PDB-4dhk: Crystal structure of a deoxycytidine triphosphate deaminase (dCTP... -

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Basic information

Entry
Database: PDB / ID: 4dhk
TitleCrystal structure of a deoxycytidine triphosphate deaminase (dCTP deaminase) from Burkholderia thailandensis
ComponentsDeoxycytidine triphosphate deaminase
KeywordsHYDROLASE / Burkholderia thailandensis / deaminase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / nucleotide binding
Similarity search - Function
dCTP deaminase / dCTP deaminase-like / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJan 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4499
Polymers43,0152
Non-polymers4347
Water2,810156
1
A: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8186
Polymers21,5071
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6313
Polymers21,5071
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,34727
Polymers129,0446
Non-polymers1,30321
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation4_455x-1/3,y+1/3,z+1/31
crystal symmetry operation5_455-y-1/3,x-y+1/3,z+1/31
crystal symmetry operation6_455-x+y-1/3,-x+1/3,z+1/31
Buried area25830 Å2
ΔGint-96 kcal/mol
Surface area33250 Å2
MethodPISA
4
A: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,45318
Polymers64,5223
Non-polymers93115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area11970 Å2
ΔGint-23 kcal/mol
Surface area19340 Å2
MethodPISA
5
B: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8949
Polymers64,5223
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8750 Å2
ΔGint-42 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.870, 92.870, 137.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Deoxycytidine triphosphate deaminase / dCTP deaminase


Mass: 21507.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: dcd, BTH_I0860 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T083, dCTP deaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Internal tracking number 225926. JCSG+ well A2. 20.0% w/v PEG3000, 0.1M Ammonium citrate/citric acid, 20% Ethylene glycol Cryo. ButhA.00973.a.A1 PS01180 46.83mg/ml, pH 5.5, VAPOR DIFFUSION, ...Details: Internal tracking number 225926. JCSG+ well A2. 20.0% w/v PEG3000, 0.1M Ammonium citrate/citric acid, 20% Ethylene glycol Cryo. ButhA.00973.a.A1 PS01180 46.83mg/ml, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→69.44 Å / Num. all: 27772 / Num. obs: 27763 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.52 % / Biso Wilson estimate: 39.228 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 22.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.05-2.14.480.4583.4916720462046100
2.1-2.160.3494.491282031100
2.16-2.220.2785.287011932100
2.22-2.290.2595.984681878100
2.29-2.370.1947.883981857100
2.37-2.450.1569.479801768100
2.45-2.540.12511.677121700100
2.54-2.650.10913.375401665100
2.65-2.760.0817.570811557100
2.76-2.90.06321.96900151599.9
2.9-3.060.04528.165921446100
3.06-3.240.03734.361501352100
3.24-3.470.03140.95749126499.9
3.47-3.740.02746.853791191100
3.74-4.10.02452.448971077100
4.1-4.580.02158.44506990100
4.58-5.290.02160.34080887100
5.29-6.480.02158.73363736100
6.48-9.170.0261256656199.6
9.170.0264.6133130897.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.44 Å
Translation2.5 Å46.44 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3km3

3km3


Resolution: 2.05→69.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.905 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1395 5 %RANDOM
Rwork0.168 ---
all0.168 27772 --
obs0.168 27761 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.05→69.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 28 156 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022658
X-RAY DIFFRACTIONr_bond_other_d0.0040.021774
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.953623
X-RAY DIFFRACTIONr_angle_other_deg1.01834309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34823.729118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32515388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1541516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213004
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02576
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 104 -
Rwork0.236 1940 -
all-2044 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77040.0097-0.06810.69210.07241.08840.00780.1825-0.1515-0.1457-0.0203-0.12340.18910.08620.01250.09080.03370.03560.0792-0.04520.0689-38.404215.781758.6087
21.275-0.3022-0.35760.8125-0.120.9646-0.0892-0.31850.16470.30850.0882-0.0158-0.24530.02530.0010.18490.03770.00190.1227-0.07180.0543-4.928513.319358.2996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 173
2X-RAY DIFFRACTION2B3 - 161

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