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- PDB-7mmq: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-N... -

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Basic information

Entry
Database: PDB / ID: 7mmq
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Reduced Hydroquinone Form
Components
  • Protein NrdI
  • Ribonucleoside-diphosphate reductase
KeywordsOxidoreductase/FMN binding Protein / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / NrdI / Beta-NrdI complex / Oxidoreductase-FMN binding Protein complex
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / FMN binding / metal ion binding / membrane
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / 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 ...Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / 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 / Flavoprotein-like superfamily / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Protein NrdI / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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
C: Ribonucleoside-diphosphate reductase
D: Ribonucleoside-diphosphate reductase
E: Protein NrdI
G: Protein NrdI
F: Protein NrdI
H: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,33115
Polymers223,2308
Non-polymers2,1027
Water3,711206
1
A: Ribonucleoside-diphosphate reductase
E: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2643
Polymers55,8072
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-15 kcal/mol
Surface area18660 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase
F: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3564
Polymers55,8072
Non-polymers5482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-19 kcal/mol
Surface area18540 Å2
MethodPISA
3
C: Ribonucleoside-diphosphate reductase
G: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3564
Polymers55,8072
Non-polymers5482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-17 kcal/mol
Surface area18290 Å2
MethodPISA
4
D: Ribonucleoside-diphosphate reductase
H: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3564
Polymers55,8072
Non-polymers5482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-21 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.385, 105.012, 138.128
Angle α, β, γ (deg.)90.000, 100.580, 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.: 4
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: Protein
Protein NrdI


Mass: 16486.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus urinae (bacteria) / Gene: nrdI, CYJ29_07405, DBT54_07500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178HGH7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.5 Å3/Da / Density % sol: 50.87 % / Mosaicity: 0.394 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% (w/v) PEG 3350, 0.2 M calcium chloride, 0.1 M Tris pH 8.5, 10 mM sodium dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 84812 / % possible obs: 98.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Χ2: 0.923 / Net I/σ(I): 7.2 / Num. measured all: 501421
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.60.77235860.5730.4260.8870.92383.4
2.44-2.494.20.74439090.6670.3830.8420.93791.1
2.49-2.534.60.68740930.7380.3420.7710.91795.4
2.53-2.5950.62141940.80.2970.6910.91897.8
2.59-2.645.40.57942460.8370.2710.6410.91799.3
2.64-2.75.70.50243380.8840.2280.5530.91399.9
2.7-2.775.90.42842580.9210.190.470.938100
2.77-2.8560.37143110.9370.1640.4060.941100
2.85-2.935.70.29742580.9530.1350.3270.9699.9
2.93-3.026.10.2442950.9680.1050.2620.956100
3.02-3.136.20.19343290.9790.0840.2110.962100
3.13-3.266.60.15242970.9870.0630.1650.951100
3.26-3.416.90.11643150.9930.0470.1260.959100
3.41-3.586.90.08642960.9950.0350.0930.964100
3.58-3.816.80.06943000.9960.0280.0750.962100
3.81-4.16.40.05343470.9970.0230.0580.917100
4.1-4.526.10.04243010.9980.0180.0460.895100
4.52-5.176.50.03843440.9980.0160.0410.88100
5.17-6.516.70.0443670.9980.0170.0430.86100
6.51-506.20.02744280.9990.0120.030.80199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6ebo


Resolution: 2.4→49.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.091 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.475 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 3983 5.1 %RANDOM
Rwork0.1983 ---
obs0.2005 74743 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.3 Å2 / Biso mean: 38.612 Å2 / Biso min: 14.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20.1 Å2
2--0.35 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.4→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14291 0 142 206 14639
Biso mean--32.29 31.4 -
Num. residues----1759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01314778
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713365
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.6420074
X-RAY DIFFRACTIONr_angle_other_deg1.0981.57431050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65951743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06423.578816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.347152463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9931568
X-RAY DIFFRACTIONr_chiral_restr0.0460.21898
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023139
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.313 169 -
Rwork0.298 3022 -
obs--49.94 %

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