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- PDB-1xjk: Structural mechanism of allosteric substrate specificity in a rib... -

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Basic information

Entry
Database: PDB / ID: 1xjk
TitleStructural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dGTP-ADP complex
Componentsribonucleotide reductase, B12-dependent
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / 10 alpha-beta barrel / allosteric regulation / substrate specificity / protein-nucleotide complex
Function / homology
Function and homology information


cobalamin binding / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA biosynthetic process / DNA replication / ATP binding
Similarity search - Function
Ribonucleotide reductase, adenosylcobalamin-dependent / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLarsson, K.-M. / Jordan, A. / Eliasson, R. / Reichard, P. / Logan, D.T. / Nordlund, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.
Authors: Larsson, K.-M. / Jordan, A. / Eliasson, R. / Reichard, P. / Logan, D.T. / Nordlund, P.
History
DepositionSep 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2012Group: Structure summary
Revision 1.4Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.5Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Authors suggest a point mutation either in the sequencing clone (SER->TYR mutation) or in ...SEQUENCE Authors suggest a point mutation either in the sequencing clone (SER->TYR mutation) or in their expression clone (TYR->SER). Codons for TYR=ATA and SER=AGA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribonucleotide reductase, B12-dependent
B: ribonucleotide reductase, B12-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,6388
Polymers146,7202
Non-polymers1,9176
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-64 kcal/mol
Surface area45830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.120, 122.860, 106.060
Angle α, β, γ (deg.)90.00, 103.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit consists of a homodimer, which constitute a functional form of the enzyme.

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Components

#1: Protein ribonucleotide reductase, B12-dependent /


Mass: 73360.203 Da / Num. of mol.: 2 / Fragment: residues 1-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nrdj / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O33839, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.55 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG8000, sodium acetate, sodium chloride, dithiotreithol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.035 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. all: 79946 / Num. obs: 77677 / % possible obs: 97.2 % / Redundancy: 2.15 % / Rsym value: 0.049 / Net I/σ(I): 8.9
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 2.15 % / Mean I/σ(I) obs: 2.48 / Rsym value: 0.289 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XJE

1xje


Resolution: 2.12→22.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.619 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25572 4113 5.1 %RANDOM
Rwork0.20499 ---
obs0.20763 76628 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.682 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å22.05 Å2
2---0.58 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.12→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9883 0 118 247 10248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210202
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.98913795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08251225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67524.232475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.813151852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9921568
X-RAY DIFFRACTIONr_chiral_restr0.1450.21540
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027583
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.25057
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.26945
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2488
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.110.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.56333
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75429930
X-RAY DIFFRACTIONr_scbond_it2.57434408
X-RAY DIFFRACTIONr_scangle_it3.844.53865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 269 -
Rwork0.286 5146 -
obs--88.74 %

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