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- PDB-1pem: Ribonucleotide Reductase Protein R1E from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 1pem
TitleRibonucleotide Reductase Protein R1E from Salmonella typhimurium
ComponentsRibonucleoside-diphosphate reductase 2 alpha chain
KeywordsOXIDOREDUCTASE / 10 stranded alpha/beta barrel / protein-specificity-effector complex / dATP
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ATP binding
Similarity search - Function
50s Ribosomal Protein L19e, Chain O, domain 1 - #20 / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal ...50s Ribosomal Protein L19e, Chain O, domain 1 - #20 / Ribonucleotide reductase N-terminal / Ribonucleotide reductase, class 1b, subunit NrdE / Ribonucleotide reductase N-terminal / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase 2 subunit alpha
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsUppsten, M. / Farnegardh, M. / Jordan, A. / Eliasson, R. / Eklund, H. / Uhlin, U.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors.
Authors: Uppsten, M. / Farnegardh, M. / Jordan, A. / Eliasson, R. / Eklund, H. / Uhlin, U.
History
DepositionMay 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 2 alpha chain


Theoretical massNumber of molelcules
Total (without water)80,6861
Polymers80,6861
Non-polymers00
Water00
1
A: Ribonucleoside-diphosphate reductase 2 alpha chain

A: Ribonucleoside-diphosphate reductase 2 alpha chain


Theoretical massNumber of molelcules
Total (without water)161,3722
Polymers161,3722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)99.079, 99.079, 290.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological homodimer is generated by the two fold axis: -y, -x, -z+1/2

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Components

#1: Protein Ribonucleoside-diphosphate reductase 2 alpha chain / Ribonucleotide reductase 2 / R1E protein


Mass: 80686.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: NRDE OR STM2807 / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q08698, ribonucleoside-diphosphate reductase

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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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: sodium malonate, magnesium chloride, DTT, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2001 / Details: mirrors
RadiationMonochromator: Double crystal,Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.99→40 Å / Num. all: 30043 / Num. obs: 30043 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 19.1
Reflection shellResolution: 2.99→3.05 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 6.6 / Rsym value: 0.42 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanin model of ribonucleotide reductase protein R1 from E.coli

Resolution: 2.99→19.96 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.076 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.601 / ESU R Free: 0.325 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24297 1518 5.1 %RANDOM
Rwork0.21754 ---
all0.2187 28433 --
obs0.21878 28433 19.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.633 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---1.04 Å20 Å2
3---2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.99→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 0 0 5447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215573
X-RAY DIFFRACTIONr_bond_other_d0.0010.024993
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9377545
X-RAY DIFFRACTIONr_angle_other_deg0.884311551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.823680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.81815977
X-RAY DIFFRACTIONr_chiral_restr0.0940.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026274
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021233
X-RAY DIFFRACTIONr_nbd_refined0.2730.31482
X-RAY DIFFRACTIONr_nbd_other0.2510.35568
X-RAY DIFFRACTIONr_nbtor_other0.0610.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.5250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1110.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.366
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.53389
X-RAY DIFFRACTIONr_mcangle_it1.27925444
X-RAY DIFFRACTIONr_scbond_it1.23232184
X-RAY DIFFRACTIONr_scangle_it2.3034.52101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.071 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 109
Rwork0.299 2019

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