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- PDB-2jaq: Structure of deoxyadenosine kinase from M. mycoides with bound dCTP -

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Basic information

Entry
Database: PDB / ID: 2jaq
TitleStructure of deoxyadenosine kinase from M. mycoides with bound dCTP
ComponentsDEOXYGUANOSINE KINASE
KeywordsTRANSFERASE / KINASE / DEOXYRIBONUCLEOSIDE KINASE
Function / homology
Function and homology information


deoxyguanosine kinase / deoxyguanosine kinase activity / ATP binding / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxyguanosine kinase
Similarity search - Component
Biological speciesMYCOPLASMA MYCOIDES SUBSP. MYCOIDES SC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWelin, M. / Wang, L. / Eriksson, S. / Eklund, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure-Function Analysis of a Bacterial Deoxyadenosine Kinase Reveals the Basis for Substrate Specificity.
Authors: Welin, M. / Wang, L. / Eriksson, S. / Eklund, H.
History
DepositionNov 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYGUANOSINE KINASE
B: DEOXYGUANOSINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5124
Polymers48,5782
Non-polymers9342
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.527, 84.527, 53.603
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARG1AA1 - 611 - 61
21METMETARGARG1BB1 - 611 - 61
12SERSERLYSLYS2AA62 - 6662 - 66
22SERSERLYSLYS2BB62 - 6662 - 66
13ASNASNLEULEU1AA73 - 11373 - 113
23ASNASNLEULEU1BB73 - 11373 - 113
14LYSLYSPHEPHE2AA122 - 125122 - 125
24LYSLYSPHEPHE2BB122 - 125122 - 125
15ASPASPILEILE1AA126 - 142126 - 142
25ASPASPILEILE1BB126 - 142126 - 142
16LYSLYSARGARG2AA143 - 145143 - 145
26LYSLYSARGARG2BB143 - 145143 - 145
17GLYGLYILEILE1AA146 - 191146 - 191
27GLYGLYILEILE1BB146 - 191146 - 191
18GLUGLULEULEU2AA192 - 193192 - 193
28GLUGLULEULEU2BB192 - 193192 - 193
19LEULEUILEILE1AA193 - 201193 - 201
29LEULEUILEILE1BB193 - 201193 - 201

NCS oper: (Code: given
Matrix: (1, -0.000937, 0.001337), (-0.000935, -1, -0.001229), (0.001338, 0.001228, -1)
Vector: -0.00986, -0.00647, -0.03373)

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Components

#1: Protein DEOXYGUANOSINE KINASE / DEOXYADENOSINE KINASE


Mass: 24288.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOPLASMA MYCOIDES SUBSP. MYCOIDES SC (bacteria)
Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93IG4, 2'-deoxyadenosine kinase, deoxyguanosine kinase
#2: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.2 Å3/Da / Density % sol: 42.4 %
Crystal growpH: 6.2 / Details: 20% PEG 3350 0.2M AMF, pH 6.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2006 / Details: MIRROR
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.3→43.25 Å / Num. obs: 18856 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.744 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 67-72 AND 116-121 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 978 5.2 %RANDOM
Rwork0.233 ---
obs0.234 18004 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 56 98 3303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9894405
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31925.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55115621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.341512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022378
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21535
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22244
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5961.51909
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00323050
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32531529
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1224.51355
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 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1509tight positional00.01
65medium positional0.240.5
1509tight thermal0.040.5
65medium thermal0.232
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 68
Rwork0.251 1332

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