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

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Basic information

Entry
Database: PDB / ID: 7mms
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Semiquinone Form with Cu(I) bound
Components
  • Protein NrdI
  • Ribonucleoside-diphosphate reductaseRibonucleotide reductase
KeywordsOxidoreductase/FMN Binding protein / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / NrdI / Beta-NrdI complex / NrdF-NrdI complex / reduced / semiquinone / 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 / protein modification process / FMN 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 small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Flavoprotein-like superfamily
Similarity search - Domain/homology
COPPER (I) ION / Chem-FNR / Protein NrdI / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 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)226,26628
Polymers223,2308
Non-polymers3,03720
Water10,881604
1
A: Ribonucleoside-diphosphate reductase
E: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6468
Polymers55,8072
Non-polymers8386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-39 kcal/mol
Surface area18740 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase
F: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7389
Polymers55,8072
Non-polymers9307
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-37 kcal/mol
Surface area18770 Å2
MethodPISA
3
C: Ribonucleoside-diphosphate reductase
G: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5257
Polymers55,8072
Non-polymers7185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-44 kcal/mol
Surface area18540 Å2
MethodPISA
4
D: Ribonucleoside-diphosphate reductase
H: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3584
Polymers55,8072
Non-polymers5502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-13 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.354, 104.787, 137.412
Angle α, β, γ (deg.)90.000, 100.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABCDEGFH

#1: Protein
Ribonucleoside-diphosphate reductase / Ribonucleotide 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

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Non-polymers , 5 types, 624 molecules

#3: Chemical
ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.89 % / Mosaicity: 0.547 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% (w/v) PEG 3350, 0.2 M calcium chloride, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 166049 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 0.932 / Net I/σ(I): 6.3 / Num. measured all: 1109241
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.91-1.945.91.20282100.6420.5261.3140.88298.3
1.94-1.986.51.04681690.7530.4311.1330.87798.4
1.98-2.026.70.8882480.8070.3610.9520.89599.4
2.02-2.066.70.72782350.8620.2990.7870.89798.8
2.06-2.16.50.61382250.8650.2590.6670.92998.9
2.1-2.156.70.49682100.9220.2060.5380.95799
2.15-2.26.80.41982770.9390.1710.4530.9599.1
2.2-2.266.50.34382960.9550.1440.3720.96699.5
2.26-2.3370.27782790.9730.1110.2980.97299.4
2.33-2.416.90.24782660.9750.10.2670.98399.4
2.41-2.496.70.19483050.980.080.210.97799.4
2.49-2.596.50.16182800.9840.0680.1740.98199.6
2.59-2.716.80.13482880.990.0550.1450.9799.7
2.71-2.856.70.10883500.9920.0440.1170.96699.7
2.85-3.0370.08783500.9940.0350.0940.95699.8
3.03-3.276.70.07283270.9950.030.0780.97599.8
3.27-3.596.90.0683680.9960.0240.0641.008100
3.59-4.1170.05283930.9970.0210.0560.959100
4.11-5.186.70.04684360.9970.0190.050.848100
5.18-506.70.04185370.9980.0170.0440.684100

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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: 1.91→49.25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.635 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.14
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 8195 5.1 %RANDOM
Rwork0.2013 ---
obs0.2026 153398 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.38 Å2 / Biso mean: 23.024 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.13 Å2
2--0.07 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.91→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14368 0 185 604 15157
Biso mean--23.88 22.93 -
Num. residues----1773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01314969
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713524
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.6420335
X-RAY DIFFRACTIONr_angle_other_deg1.1371.57531441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57551778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96623.633823
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.884152490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4481568
X-RAY DIFFRACTIONr_chiral_restr0.050.21915
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023164
LS refinement shellResolution: 1.91→1.956 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.303 421 -
Rwork0.285 7891 -
obs--67.29 %

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