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

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Basic information

Entry
Database: PDB / ID: 7mmr
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Oxidized Form with Cu(I) bound
Components
  • Protein NrdI
  • Ribonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE/FMN Binding Protein / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / NrdI / FLAVOPROTEIN / 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
COPPER (I) ION / FLAVIN MONONUCLEOTIDE / Protein NrdI / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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

Downloads & links

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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)222,12935
Polymers218,7778
Non-polymers3,35327
Water9,530529
1
A: Ribonucleoside-diphosphate reductase
E: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4107
Polymers54,6942
Non-polymers7165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-38 kcal/mol
Surface area18760 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase
F: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5028
Polymers54,6942
Non-polymers8086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-51 kcal/mol
Surface area19130 Å2
MethodPISA
3
C: Ribonucleoside-diphosphate reductase
G: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,71612
Polymers54,6942
Non-polymers1,02210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-80 kcal/mol
Surface area18750 Å2
MethodPISA
4
D: Ribonucleoside-diphosphate reductase
H: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5028
Polymers54,6942
Non-polymers8086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-51 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.398, 104.958, 138.067
Angle α, β, γ (deg.)90.000, 100.010, 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


Mass: 38764.375 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: 15929.860 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 , 6 types, 556 molecules

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


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.52 Å3/Da / Density % sol: 51.27 % / Mosaicity: 0.499 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% (w/v) PEG 3350, 0.1 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: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 146267 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Χ2: 0.9 / Net I/σ(I): 9.3 / Num. measured all: 1050183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.036.81.02672450.7580.4171.1090.80198.9
2.03-2.076.90.81872210.8030.3320.8840.85499.2
2.07-2.116.90.69372250.8460.2810.7490.86399.3
2.11-2.1570.58173080.8960.2340.6270.8799.4
2.15-2.270.60872410.9070.2440.6560.88299.3
2.2-2.2570.35172960.9280.1410.3791.08599.3
2.25-2.3170.34572450.9560.1380.3730.98999.7
2.31-2.377.10.33573180.9640.1340.3620.999.8
2.37-2.447.10.24772850.9750.0990.2660.89999.7
2.44-2.527.10.19973110.980.080.2150.88799.8
2.52-2.617.10.16773170.9840.0670.180.89799.8
2.61-2.717.20.13772940.9890.0550.1480.90299.9
2.71-2.847.20.1173150.9920.0440.1180.87799.9
2.84-2.997.30.08673420.9940.0340.0930.86299.9
2.99-3.177.40.07273500.9950.0280.0770.914100
3.17-3.427.50.06573150.9950.0250.071.036100
3.42-3.767.50.05873650.9960.0220.0621.198100
3.76-4.317.50.04773890.9970.0180.050.975100
4.31-5.437.40.03873960.9980.0150.040.715100
5.43-507.60.03574890.9990.0130.0370.60599.7

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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→34.32 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.382 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.16
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 7260 5 %RANDOM
Rwork0.2087 ---
obs0.21 137118 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.47 Å2 / Biso mean: 27.852 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20.14 Å2
2---0.09 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14435 0 153 529 15117
Biso mean--28.22 27.98 -
Num. residues----1783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01315032
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713585
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.65320429
X-RAY DIFFRACTIONr_angle_other_deg1.1141.58131580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48851787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03423.648825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.039152502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2711568
X-RAY DIFFRACTIONr_chiral_restr0.0470.21928
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023167
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.312 469 -
Rwork0.276 8893 -
obs--86.75 %

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