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

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Basic information

Entry
Database: PDB / ID: 1xje
TitleStructural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex
Componentsribonucleotide reductase, B12-dependent
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / 10 alpha-beta barrel / protein-nucleotide complex / substrate specificity / allosteric regulation
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
GUANOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Residue 205 is a tyrosine in GB NP_227934 but no density for atoms beyond CB can be found ...SEQUENCE Residue 205 is a tyrosine in GB NP_227934 but no density for atoms beyond CB can be found in an otherwise ordered loop, suggesting sequencing error or spontaneous mutation. The 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

Downloads & links

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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)148,7409
Polymers146,7482
Non-polymers1,9917
Water14,250791
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-66 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.391, 124.376, 107.243
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit consists of a dimer which is the apparent biological unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ribonucleotide reductase, B12-dependent /


Mass: 73374.234 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

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Non-polymers , 5 types, 798 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.63 Å3/Da / Density % sol: 53.32 %
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.9→18 Å / Num. obs: 119507 / % possible obs: 97.2 % / Redundancy: 2.7 % / Rsym value: 0.07 / Net I/σ(I): 12.23
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.399 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1R1R

1r1r


Resolution: 1.9→18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.478 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22268 5794 5 %RANDOM
Rwork0.18241 ---
obs0.18445 110169 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.972 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å21.3 Å2
2--0.4 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10001 0 122 791 10914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210325
X-RAY DIFFRACTIONr_bond_other_d0.0010.029510
X-RAY DIFFRACTIONr_angle_refined_deg1.781.98813959
X-RAY DIFFRACTIONr_angle_other_deg0.9483.00122087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89851240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7324.012481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.342151876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6571574
X-RAY DIFFRACTIONr_chiral_restr0.1250.21553
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022075
X-RAY DIFFRACTIONr_nbd_refined0.2210.22213
X-RAY DIFFRACTIONr_nbd_other0.1870.29773
X-RAY DIFFRACTIONr_nbtor_refined0.1830.25054
X-RAY DIFFRACTIONr_nbtor_other0.0890.26075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3751.58037
X-RAY DIFFRACTIONr_mcbond_other0.2671.52511
X-RAY DIFFRACTIONr_mcangle_it1.595210038
X-RAY DIFFRACTIONr_scbond_it2.63334805
X-RAY DIFFRACTIONr_scangle_it3.664.53921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 432 -
Rwork0.233 8045 -
obs--96.67 %

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