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

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Basic information

Entry
Database: PDB / ID: 1xjg
TitleStructural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-UDP 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 / 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 / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, barrel domain / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

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)148,5888
Polymers146,7482
Non-polymers1,8396
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-60 kcal/mol
Surface area45660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.537, 123.514, 105.886
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

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
11METMETTYRTYR6AA1 - 621 - 62
21METMETTYRTYR6BB1 - 621 - 62
32ILEILEGLYGLY6AA71 - 17971 - 179
42ILEILEGLYGLY6BB71 - 17971 - 179
53LEULEUTYRTYR6AA211 - 512211 - 512
63LEULEUTYRTYR6BB211 - 512211 - 512
74PHEPHELEULEU4AA569 - 633569 - 633
84PHEPHELEULEU4BB569 - 633569 - 633

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.58 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: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 48781 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rsym value: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 3.77 / Rsym value: 0.38 / % possible all: 100

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Processing

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

1xje


Resolution: 2.5→24.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.365 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.561 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26366 2628 5.1 %RANDOM
Rwork0.19454 ---
obs0.19816 48781 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.037 Å2
Baniso -1Baniso -2Baniso -3
1-6.26 Å20 Å22.51 Å2
2---2.29 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9849 0 112 248 10209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210158
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.98813733
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6451216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05224.14471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98151845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9461568
X-RAY DIFFRACTIONr_chiral_restr0.1360.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.25413
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.26952
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2537
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.470.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9941.56301
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70829881
X-RAY DIFFRACTIONr_scbond_it2.38934402
X-RAY DIFFRACTIONr_scangle_it3.624.53852
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
517medium positional0.180.5
3752loose positional0.375
517medium thermal1.482
3752loose thermal5.510
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 190 -
Rwork0.26 3554 -
obs--100 %

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