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

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Basic information

Entry
Database: PDB / ID: 1xjn
TitleStructural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-CDP 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
CYTIDINE-5'-DIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 6, 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_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_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
C: ribonucleotide reductase, B12-dependent
D: ribonucleotide reductase, B12-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,11013
Polymers293,4974
Non-polymers3,6139
Water11,692649
1
A: ribonucleotide reductase, B12-dependent
B: ribonucleotide reductase, B12-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5737
Polymers146,7482
Non-polymers1,8245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-46 kcal/mol
Surface area46140 Å2
MethodPISA
2
C: ribonucleotide reductase, B12-dependent
D: ribonucleotide reductase, B12-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5376
Polymers146,7482
Non-polymers1,7894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-38 kcal/mol
Surface area45740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.970, 123.830, 117.410
Angle α, β, γ (deg.)90.00, 104.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit consists of two homodimers. The homodimer constitute is the smallest functional unit.

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Components

#1: Protein
ribonucleotide reductase, B12-dependent /


Mass: 73374.234 Da / Num. of mol.: 4 / 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-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
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: 0.8126 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 139338 / Num. obs: 138333 / % possible obs: 99.3 % / Redundancy: 3 % / Rsym value: 0.097 / Net I/σ(I): 8
Reflection shellResolution: 2.25→2.5 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.368 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XJE

1xje


Resolution: 2.25→19.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.822 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25391 6927 5 %RANDOM
Rwork0.18983 ---
obs0.19303 131406 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å21.48 Å2
2---1.08 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19664 0 221 649 20534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02220281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.98827417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46652430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22624.19945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.284153672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.98615136
X-RAY DIFFRACTIONr_chiral_restr0.1330.23062
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.29811
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.213685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2983
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.512626
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.767219735
X-RAY DIFFRACTIONr_scbond_it2.65438755
X-RAY DIFFRACTIONr_scangle_it4.0884.57682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 485 -
Rwork0.234 9625 -
obs--99.8 %

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