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- PDB-7mmp: Crystal Structure of the Class Ie Ribonucleotide Reductase -

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Basic information

Entry
Database: PDB / ID: 7mmp
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase
Components
  • Protein NrdI
  • Ribonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free
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: 2.15 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)225,25617
Polymers223,2308
Non-polymers2,0269
Water8,161453
1
A: Ribonucleoside-diphosphate reductase
E: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3044
Polymers55,8072
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-34 kcal/mol
Surface area19450 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase
F: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3044
Polymers55,8072
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-28 kcal/mol
Surface area18890 Å2
MethodPISA
3
C: Ribonucleoside-diphosphate reductase
G: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3445
Polymers55,8072
Non-polymers5373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-28 kcal/mol
Surface area18750 Å2
MethodPISA
4
D: Ribonucleoside-diphosphate reductase
H: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3044
Polymers55,8072
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-27 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.656, 105.331, 138.894
Angle α, β, γ (deg.)90.000, 100.460, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#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.: 453 / 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: 50.85 % / Mosaicity: 0.082 °
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-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 116972 / % possible obs: 97.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.059 / Rrim(I) all: 0.127 / Χ2: 0.895 / Net I/σ(I): 6.5 / Num. measured all: 479235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.60.553080.720.3440.6120.84889.1
2.19-2.232.90.48755680.7240.3220.5890.83793.7
2.23-2.273.30.45957660.7760.2850.5440.86697
2.27-2.323.70.42858250.8240.2490.4980.85997.4
2.32-2.3740.40858270.8580.2260.4690.85997.7
2.37-2.424.10.35358800.8960.1910.4040.84598.1
2.42-2.484.20.3258540.9040.1720.3650.86998.5
2.48-2.554.10.29558370.9070.1610.3380.88498.2
2.55-2.624.20.27958850.9230.1490.3180.90198.1
2.62-2.714.30.24258550.9490.1280.2750.92298.3
2.71-2.814.40.20958900.9560.1090.2370.93598.4
2.81-2.924.70.18758970.9690.0950.2110.95898.7
2.92-3.054.60.15959250.9690.0810.1790.99498.8
3.05-3.214.50.12759000.9790.0650.1430.9898.7
3.21-3.414.40.10759360.9830.0560.1210.98198.6
3.41-3.684.10.08659240.9850.0470.0990.94298.9
3.68-4.054.30.07858940.9880.0410.0880.90398.4
4.05-4.634.60.0759500.990.0350.0780.87398.7
4.63-5.834.60.06859980.990.0340.0770.8399.1
5.83-504.30.06260530.9910.0320.070.72198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EBO

6ebo


Resolution: 2.15→49.65 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.889 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.186
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 5767 5 %RANDOM
Rwork0.1948 ---
obs0.1963 108656 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.66 Å2 / Biso mean: 28.976 Å2 / Biso min: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0.05 Å2
2---0.17 Å2-0 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 2.15→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14552 0 98 453 15103
Biso mean--22.95 26.68 -
Num. residues----1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01315031
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713550
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.65320428
X-RAY DIFFRACTIONr_angle_other_deg1.1731.58131483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97551785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71423.646831
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.339152493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5041568
X-RAY DIFFRACTIONr_chiral_restr0.0550.21930
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023182
LS refinement shellResolution: 2.15→2.203 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.295 301 -
Rwork0.287 5980 -
obs--71.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.39450.04040.04650.62720.06770.221-0.0542-0.01840.03320.07120.05960.0798-0.02640.001-0.00540.0837-0.02340.01080.10260.02710.067223.317223.395630.2857
20.51250.059-0.00890.50310.03670.2183-0.0750.0748-0.0756-0.0560.0659-0.00110.06930.04330.00910.098-0.04220.00320.1071-0.00050.06132.99861.84510.8128
30.5620.01520.13220.26270.0770.2877-0.05440.1189-0.0332-0.02630.04940.0416-0.0108-0.00920.0050.0711-0.00680.03280.10450.04470.083415.7915-28.724936.8693
40.58240.010.00540.0852-0.01930.5036-0.0595-0.10030.05230.00280.0095-0.0067-0.11690.04570.050.0898-0.00190.01750.09420.03560.085725.7002-13.203761.4956
51.9401-0.38130.21821.10680.01120.955-0.0943-0.00890.1137-0.0730.00650.1789-0.1199-0.03860.08780.02580.0061-0.03940.03320.02850.1725-0.09932.921220.3867
62.07560.258-0.12721.61630.07840.979-0.08810.0311-0.24260.0015-0.00410.24630.1045-0.06880.09220.0315-0.03150.0410.07340.00880.1692-7.4975-40.596544.1997
71.39360.0324-0.3461.2234-0.39231.5784-0.10110.1214-0.0517-0.12190.0455-0.12030.05050.10810.05570.0464-0.03950.04220.1394-0.04620.04256.367311.10650.4843
82.0409-0.47880.2720.7952-0.10661.6427-0.183-0.3978-0.0720.0140.11830.02480.03760.30050.06470.02040.04730.01040.27240.0720.025948.7574-24.647568.9902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 337
2X-RAY DIFFRACTION2B4 - 337
3X-RAY DIFFRACTION3C4 - 337
4X-RAY DIFFRACTION4D4 - 337
5X-RAY DIFFRACTION5E2 - 140
6X-RAY DIFFRACTION6G3 - 139
7X-RAY DIFFRACTION7F3 - 139
8X-RAY DIFFRACTION8H3 - 140

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