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- PDB-6dqx: Actinobacillus ureae class Id ribonucleotide reductase alpha subunit -

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Basic information

Entry
Database: PDB / ID: 6dqx
TitleActinobacillus ureae class Id ribonucleotide reductase alpha subunit
ComponentsRibonucleoside-diphosphate reductase, alpha chainRibonucleotide reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase / alpha subunit / class Id / nucleotide metabolism
Function / homologyRibonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase alpha chain / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase, barrel domain / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / Ribonucleoside-diphosphate reductase, alpha chain
Function and homology information
Biological speciesActinobacillus ureae ATCC 25976 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMcBride, M.J. / Palowitch, G.M. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM119707 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis.
Authors: Rose, H.R. / Maggiolo, A.O. / McBride, M.J. / Palowitch, G.M. / Pandelia, M.E. / Davis, K.M. / Yennawar, N.H. / Boal, A.K.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase, alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,70310
Polymers65,2441
Non-polymers4609
Water4,666259
1
A: Ribonucleoside-diphosphate reductase, alpha chain
hetero molecules

A: Ribonucleoside-diphosphate reductase, alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,40720
Polymers130,4872
Non-polymers92018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_935-x+4,-y-2,z1
Unit cell
γ
α
β
Length a, b, c (Å)97.984, 97.984, 132.005
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Ribonucleoside-diphosphate reductase, alpha chain / Ribonucleotide reductase


Mass: 65243.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus ureae ATCC 25976 (bacteria)
Gene: HMPREF0027_1834 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: E8KJ17, ribonucleoside-diphosphate reductase

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Chloride
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Ethylene glycol
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 4000, 0.2 M magnesium chloride, 0.1 M tris base pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 62864 / % possible obs: 97.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Χ2: 0.931 / Net I/σ(I): 11.9 / Num. measured all: 450739
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.794.80.5427220.890.2670.6050.87586
1.79-1.825.70.49731560.920.2240.5470.88799.8
1.82-1.866.70.43231540.9580.1780.4690.89899.9
1.86-1.97.70.37231650.9670.1430.40.93599.8
1.9-1.947.80.30431700.9820.1150.3260.944100
1.94-1.9880.24931560.9850.0930.2660.943100
1.98-2.038.10.20431720.9890.0760.2180.94299.9
2.03-2.097.90.16531850.9910.0610.1760.97899.9
2.09-2.157.80.13631650.9930.0510.1460.95599.8
2.15-2.227.50.11131660.9940.0430.1190.97999.8
2.22-2.37.80.09731720.9950.0370.1041.00499.7
2.3-2.397.50.08232020.9950.0320.0880.95399.3
2.39-2.580.06931560.9970.0260.0740.94899.3
2.5-2.637.70.05931720.9970.0230.0630.91599.2
2.63-2.797.30.04831810.9980.0190.0520.88698.6
2.79-3.016.80.03931820.9980.0170.0430.87698.1
3.01-3.316.60.03331400.9970.0150.0370.85296.9
3.31-3.796.60.0330770.9980.0140.0340.9194.1
3.79-4.786.10.0330000.9970.0150.0330.96890.5
4.78-506.60.0333710.9980.0130.0330.89995.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DQW
Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.322 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 3122 5.1 %RANDOM
Rwork0.1915 ---
Obs0.1932 57504 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.27 Å2 / Biso mean: 23.212 Å2 / Biso min: 9.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.76→78.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 26 259 4462
Biso mean--40.82 26.55 -
Num. residues----520
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.010.0194291
r_bond_other_d0.0020.023880
r_angle_refined_deg1.3771.9535780
r_angle_other_deg0.96839024
r_dihedral_angle_1_deg5.6055515
r_dihedral_angle_2_deg39.04324.354209
r_dihedral_angle_3_deg12.03715745
r_dihedral_angle_4_deg19.9531521
r_chiral_restr0.0840.2615
r_gen_planes_refined0.0060.024739
r_gen_planes_other0.0010.02902
LS refinement shellResolution: 1.764→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 183 -
Rwork0.261 3322 -
All-3505 -
Obs--75.51 %

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