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- PDB-2j4h: Crystal structure of a H121A Escherichia coli dCTP deaminase muta... -

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Basic information

Entry
Database: PDB / ID: 2j4h
TitleCrystal structure of a H121A Escherichia coli dCTP deaminase mutant enzyme
ComponentsDEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
KeywordsHYDROLASE / DCTP DEAMINASE / NUCLEOTIDE METABOLISM / TRIMER
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
DEOXYCYTIDINE DIPHOSPHATE / dCTP deaminase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 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
DepositionAug 31, 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 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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)43,2908
Polymers42,4182
Non-polymers8726
Water00
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)64,93512
Polymers63,6283
Non-polymers1,3079
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area12820 Å2
ΔGint-72.7 kcal/mol
Surface area23240 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)64,93512
Polymers63,6283
Non-polymers1,3079
Water0
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 area12630 Å2
ΔGint-73.4 kcal/mol
Surface area22530 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.545, 62.545, 342.444
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 5
2111B1 - 5
1211A7 - 8
2211B7 - 8
1311A10 - 13
2311B10 - 13
1411A15 - 19
2411B15 - 19
1511A21 - 35
2511B21 - 35
1611A37 - 39
2611B37 - 39
1711A41 - 55
2711B41 - 55
1811A57 - 64
2811B57 - 64
1911A67 - 76
2911B67 - 76
11011A78 - 105
21011B78 - 105
11111A107 - 124
21111B107 - 124
11211A126 - 171
21211B126 - 171
11311A194
21311B194

NCS oper: (Code: given
Matrix: (-0.8738, 0.4863, 0.000542), (0.4863, 0.8738, -0.00739), (-0.004067, 0.006193, -1)
Vector: 36.05, 1.061, 85.71)

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Components

#1: Protein DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / DCTP DEAMINASE


Mass: 21209.186 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-YYY / DEOXYCYTIDINE DIPHOSPHATE


Mass: 387.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 121 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 121 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: 2.55 Å3/Da / Density % sol: 51.39 %
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: 2.7→50 Å / Num. obs: 11131 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.3 / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.605 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 563 5.1 %RANDOM
Rwork0.225 ---
obs0.228 10539 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å20 Å2
2--2.28 Å20 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 52 0 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212764
X-RAY DIFFRACTIONr_bond_other_d0.0020.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9883766
X-RAY DIFFRACTIONr_angle_other_deg0.91136008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76522.241116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54215438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1291530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023066
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
X-RAY DIFFRACTIONr_nbd_refined0.2110.2499
X-RAY DIFFRACTIONr_nbd_other0.1990.22510
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.070.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.248
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.2240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9561.52160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06122760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.30331179
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0934.51006
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: 2417 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.10.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 29
Rwork0.321 562

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