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- PDB-2j4q: Crystal structure of a E138A Escherichia coli dCTP deaminase muta... -

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Basic information

Entry
Database: PDB / ID: 2j4q
TitleCrystal structure of a E138A Escherichia coli dCTP deaminase mutant enzyme in complex with dTTP
ComponentsDEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
KeywordsHYDROLASE / NUCLEOTIDE METABOLISM / TRIMER / DCTP DEAMINASE
Function / homology
Function and homology information


dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homotrimerization / response to radiation / nucleotide binding / protein-containing complex ...dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homotrimerization / response to radiation / nucleotide binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
dCTP deaminase / dCTP deaminase-like / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / dCTP deaminase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJohansson, E. / Thymark, M. / Bynck, J.H. / Fanoe, M. / Larsen, S. / Willemoes, M.
CitationJournal: FEBS J. / Year: 2007
Title: Regulation of Dctp Deaminase from Escherichia Coli by Nonallosteric Dttp Binding to an Inactive Form of the Enzyme
Authors: Johansson, E. / Thymark, M. / Bynck, J.H. / Fanoe, M. / Larsen, S. / Willemoes, M.
History
DepositionSep 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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)43,3455
Polymers42,4362
Non-polymers9093
Water905
1
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)64,8616
Polymers63,6553
Non-polymers1,2073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area12360 Å2
ΔGint-67.1 kcal/mol
Surface area24200 Å2
MethodPQS
2
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)65,1749
Polymers63,6553
Non-polymers1,5196
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation2_545-y,x-y-1,z1
Buried area12190 Å2
ΔGint-67.1 kcal/mol
Surface area24200 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.594, 61.594, 344.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21B-2003-

HOH

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

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASPAA1 - 51 - 5
21METMETASPASPBB1 - 51 - 5
12ASPASPILEILEAA7 - 87 - 8
22ASPASPILEILEBB7 - 87 - 8
13ALAALAASPASPAA10 - 1310 - 13
23ALAALAASPASPBB10 - 1310 - 13
14GLYGLYILEILEAA15 - 1915 - 19
24GLYGLYILEILEBB15 - 1915 - 19
15PROPROVALVALAA21 - 3521 - 35
25PROPROVALVALBB21 - 3521 - 35
16LEULEUASNASNAA37 - 3937 - 39
26LEULEUASNASNBB37 - 3937 - 39
17PHEPHEASPASPAA41 - 5341 - 53
27PHEPHEASPASPBB41 - 5341 - 53
18ARGARGASPASPAA67 - 7667 - 76
28ARGARGASPASPBB67 - 7667 - 76
19GLYGLYGLYGLYAA78 - 10578 - 105
29GLYGLYGLYGLYBB78 - 10578 - 105
110LEULEUVALVALAA107 - 120107 - 120
210LEULEUVALVALBB107 - 120107 - 120
111ARGARGTYRTYRAA126 - 171126 - 171
211ARGARGTYRTYRBB126 - 171126 - 171

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Components

#1: Protein DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / DCTP DEAMINASE


Mass: 21218.221 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P28248, dCTP deaminase
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 138 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 138 TO ALA

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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: 2.5 Å3/Da / Density % sol: 50.34 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 6.8
Details: VAPOUR DIFFUSION, 34% PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH6.8, 5MM DCTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.046
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.046 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12085 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 21.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XS1

1xs1


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.067 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 1.388 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.302 582 4.8 %RANDOM
Rwork0.247 ---
obs0.25 11438 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å21.13 Å20 Å2
2--2.26 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 55 5 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212755
X-RAY DIFFRACTIONr_bond_other_d0.0020.022579
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9913756
X-RAY DIFFRACTIONr_angle_other_deg1.02735941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5435343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01722.018114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01715434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7811530
X-RAY DIFFRACTIONr_chiral_restr0.2420.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02564
X-RAY DIFFRACTIONr_nbd_refined0.2270.2508
X-RAY DIFFRACTIONr_nbd_other0.1970.22548
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.21727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.270
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.2291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0821.52170
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2222751
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66631179
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5244.51005
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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 / Number: 2193 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.10.5
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 27
Rwork0.301 591

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