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- PDB-7mmv: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta S... -

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Basic information

Entry
Database: PDB / ID: 7mmv
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae with Cu(I) bound (Cu sulfate soak)
ComponentsRibonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / METAL BINDING PROTEIN
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (I) ION / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsPalowitch, G.M. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To be published
Title: Ribonucleotide Reductas
Authors: Palowitch, G.M. / Boal, A.K.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
B: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,09510
Polymers78,6422
Non-polymers4538
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-107 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.735, 46.743, 133.922
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonucleoside-diphosphate reductase


Mass: 39320.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus urinae (strain ACS-120-V-Col10a) (bacteria)
Strain: ACS-120-V-Col10a / Gene: HMPREF9243_0731 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2I8X9, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.49 % / Mosaicity: 0.152 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 18% (w/v) PEG 3350, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 62957 / % possible obs: 98 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.058 / Rrim(I) all: 0.158 / Χ2: 0.929 / Net I/σ(I): 6.7 / Num. measured all: 462174
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.816.40.95730560.8250.41.0380.7796.7
1.81-1.846.60.9130850.860.3750.9850.76296.8
1.84-1.886.80.84631090.8910.3440.9140.81597
1.88-1.926.80.75630920.9120.3080.8170.93497
1.92-1.9670.64930770.9180.2620.7011.0497.1
1.96-27.10.53831050.9530.2140.5790.8997.4
2-2.057.30.46331210.9680.1820.4980.94397.5
2.05-2.117.30.41631040.9680.1640.4471.08397.4
2.11-2.177.50.32931250.980.1280.3530.97897.7
2.17-2.247.60.28831450.9840.1120.3090.98398
2.24-2.327.60.2631230.9820.1010.2791.0897.8
2.32-2.427.70.21731310.9890.0830.2330.96198.2
2.42-2.537.70.17631620.9920.0670.1880.93498.4
2.53-2.667.70.16131560.9920.0620.1730.93398.5
2.66-2.837.70.1331830.9930.050.1390.99298.5
2.83-3.047.70.10231660.9940.0390.1090.96198.9
3.04-3.357.70.08432390.9950.0320.091.03699
3.35-3.837.60.06331950.9970.0250.0680.93699.1
3.83-4.837.50.0532370.9970.0190.0530.77299.4
4.83-507.30.04633460.9960.0180.050.72299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EBO

6ebo


Resolution: 1.78→38.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.479 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 3053 4.9 %RANDOM
Rwork0.1801 ---
obs0.1815 59842 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.57 Å2 / Biso mean: 19.261 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.1 Å2
2---0.05 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.78→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5065 0 18 299 5382
Biso mean--31.97 24.55 -
Num. residues----622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135292
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174801
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.6397199
X-RAY DIFFRACTIONr_angle_other_deg1.2211.57111164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00323.646288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43415896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2381523
X-RAY DIFFRACTIONr_chiral_restr0.0580.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021138
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 215 -
Rwork0.248 4307 -
all-4522 -
obs--95.99 %

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