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

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Basic information

Entry
Database: PDB / ID: 1xjm
TitleStructural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP 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
TSCPD domain / TSCPD domain / Ribonucleotide reductase, adenosylcobalamin-dependent / : / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal ...TSCPD domain / TSCPD domain / Ribonucleotide reductase, adenosylcobalamin-dependent / : / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / 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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 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)148,7268
Polymers146,7482
Non-polymers1,9776
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-62 kcal/mol
Surface area45430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.438, 123.776, 106.241
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1146-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYRAA1 - 621 - 62
21METMETTYRTYRBB1 - 621 - 62
32ILEILEGLYGLYAA71 - 17971 - 179
42ILEILEGLYGLYBB71 - 17971 - 179
53LEULEUTYRTYRAA211 - 512211 - 512
63LEULEUTYRTYRBB211 - 512211 - 512
74PHEPHELEULEUAA569 - 633569 - 633
84PHEPHESERSERBB569 - 632569 - 632
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: 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-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 0.804 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.804 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 58198 / Num. obs: 57953 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rsym value: 0.115 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.337 / % possible all: 99.5

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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: 2.4→19.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.09 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24654 2969 5.1 %RANDOM
Rwork0.18444 ---
obs0.18767 54841 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.402 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å21.32 Å2
2--0.35 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9828 0 118 300 10246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.98913712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77951217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17624.246471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.609151843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7331567
X-RAY DIFFRACTIONr_chiral_restr0.1150.21533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027532
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.24993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26890
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2524
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2760.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4840.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8751.56315
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53529877
X-RAY DIFFRACTIONr_scbond_it2.33734354
X-RAY DIFFRACTIONr_scangle_it3.6314.53835
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
2120tight positional0.070.05
2134loose positional0.395
2120tight thermal0.180.5
2134loose thermal1.6310
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 234 -
Rwork0.222 3958 -
obs--99.36 %

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