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

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Basic information

Entry
Database: PDB / ID: 7mmu
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae with Cu(I) bound (Cu acetonitrile 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: 2.08 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 Reductase
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)78,9118
Polymers78,6422
Non-polymers2696
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-108 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.616, 46.766, 134.077
Angle α, β, γ (deg.)90.000, 90.520, 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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 158 / 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: 42.45 % / Mosaicity: 2.505 °
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: 2.08→50 Å / Num. obs: 40359 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.114 / Rrim(I) all: 0.269 / Χ2: 0.758 / Net I/σ(I): 4.5 / Num. measured all: 212942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.124.90.720230.7750.3380.780.62199.6
2.12-2.1550.66419830.7310.3220.740.63599.4
2.15-2.25.10.56519430.8350.2690.6280.63799.7
2.2-2.245.10.59320650.8340.2830.6590.679100
2.24-2.295.20.50319820.8670.2360.5580.668100
2.29-2.345.20.49220010.8990.2340.5470.647100
2.34-2.45.30.48319800.910.2240.5340.636100
2.4-2.475.40.51320230.7830.2420.5690.642100
2.47-2.545.40.4320200.9060.1980.4750.683100
2.54-2.625.40.47219900.8950.2230.5240.799.9
2.62-2.715.40.36820040.9350.1680.4060.691100
2.71-2.825.40.30520240.9510.140.3360.70299.9
2.82-2.955.40.29220230.9410.1340.3220.762100
2.95-3.115.40.25720080.9430.1190.2840.7599.8
3.11-3.35.40.21920060.9550.1010.2420.83699.9
3.3-3.565.40.17720440.9760.0830.1960.87799.9
3.56-3.915.40.16120230.8720.0760.1790.862100
3.91-4.485.40.13620450.9840.0650.1510.994100
4.48-5.645.30.1320430.9870.0620.1440.90299.7
5.64-505.10.13821290.9820.0690.1551.18499.3

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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: 2.08→44.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.973 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2003 5 %RANDOM
Rwork0.1946 ---
obs0.1961 37967 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.51 Å2 / Biso mean: 25.797 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.46 Å2
2--0.08 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.08→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 6 158 5223
Biso mean--26.39 25.88 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174727
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.647073
X-RAY DIFFRACTIONr_angle_other_deg1.1441.57110983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5845623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34523.579285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00115884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1041523
X-RAY DIFFRACTIONr_chiral_restr0.0490.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021121
LS refinement shellResolution: 2.08→2.132 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.281 127 -
Rwork0.232 2611 -
obs--90.84 %

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