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- PDB-3km3: Crystal structure of eoxycytidine triphosphate deaminase from ana... -

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Basic information

Entry
Database: PDB / ID: 3km3
TitleCrystal structure of eoxycytidine triphosphate deaminase from anaplasma phagocytophilum at 2.1A resolution
ComponentsDeoxycytidine triphosphate deaminase
KeywordsHYDROLASE / SSGCID / NIH / NIAID / SBRI / UW / DECODE / DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / ANAPLASMA PHAGOCYTOPHILUM / IODIDE PHASING / Nucleotide metabolism / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dCTP deaminase / dCTP catabolic process / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleotide binding
Similarity search - Function
dCTP deaminase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / dCTP deaminase
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Struct.Funct.Genom. / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,83218
Polymers45,8022
Non-polymers2,03016
Water3,171176
1
A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,49754
Polymers137,4066
Non-polymers6,09148
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area27170 Å2
ΔGint-161 kcal/mol
Surface area31270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.660, 84.660, 140.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-248-

HOH

21B-233-

HOH

31B-242-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A-1 - 158
2115B-1 - 158

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Components

#1: Protein Deoxycytidine triphosphate deaminase / dCTP deaminase


Mass: 22901.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: dcd, APH_0130 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GLJ4, dCTP deaminase
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 290 K / pH: 8.1
Details: MD PACT SCREEN CONDITION D9: 100MM TRIS PH 8.1, 200MM LICL, 20% PEG 3350; ANPHA.00973.A AT XXMG/ ML, CRYSTAL SOAKED IN 100MM HEPES PH 7.0, 200MM NACL, 20% PEG 3350, 1M KI, VAPOR DIFFUSION, ...Details: MD PACT SCREEN CONDITION D9: 100MM TRIS PH 8.1, 200MM LICL, 20% PEG 3350; ANPHA.00973.A AT XXMG/ ML, CRYSTAL SOAKED IN 100MM HEPES PH 7.0, 200MM NACL, 20% PEG 3350, 1M KI, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 21725 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 23.99
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 5.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.615 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic plus TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1124 5.1 %RANDOM
Rwork0.182 ---
obs0.184 20752 99.6 %-
all-21876 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å2-0 Å2
2--0.49 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 16 176 2636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222557
X-RAY DIFFRACTIONr_bond_other_d0.0010.021722
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9483483
X-RAY DIFFRACTIONr_angle_other_deg0.87834187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58623.303109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89915389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2531512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7711.51595
X-RAY DIFFRACTIONr_mcbond_other0.2261.5642
X-RAY DIFFRACTIONr_mcangle_it1.3922587
X-RAY DIFFRACTIONr_scbond_it2.3533962
X-RAY DIFFRACTIONr_scangle_it3.4264.5891
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
911medium positional0.140.5
1063loose positional0.385
911medium thermal0.642
1063loose thermal0.810
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 91 -
Rwork0.214 1494 -
obs--96.71 %
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)
10.7670.0197-0.2760.7394-0.2141.9072-0.0359-0.0254-0.01250.03920.0030.14410.0014-0.2330.03290.01210.00730.02290.0736-0.00590.058328.75624.964170.243
21.70650.1196-0.32592.1353-0.30381.325-0.01540.52740.2543-0.54520.02630.246-0.0715-0.1973-0.0110.21830.0064-0.08870.22690.08540.075332.38533.449124.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 158
2X-RAY DIFFRACTION1A186 - 193
3X-RAY DIFFRACTION1A194 - 305
4X-RAY DIFFRACTION2B0 - 157
5X-RAY DIFFRACTION2B186 - 193
6X-RAY DIFFRACTION2B194 - 257

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