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- PDB-3rsr: Crystal Structure of 5-NITP Inhibition of Yeast Ribonucleotide Re... -

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Basic information

Entry
Database: PDB / ID: 3rsr
TitleCrystal Structure of 5-NITP Inhibition of Yeast Ribonucleotide Reductase
ComponentsRibonucleoside-diphosphate reductase large chain 1
KeywordsOXIDOREDUCTASE / 10-stranded alpha/beta barrel / nucleotide reduction / oxidized
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal ...Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-N5P / Ribonucleoside-diphosphate reductase large chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWan, Q. / Mohammed, F. / Jha, S. / Motea, E. / Berdis, A. / Dealwis, C.G.
CitationJournal: Mol.Cancer Ther. / Year: 2012
Title: Evaluating the therapeutic potential of a non-natural nucleotide that inhibits human ribonucleotide reductase.
Authors: Ahmad, M.F. / Wan, Q. / Jha, S. / Motea, E. / Berdis, A. / Dealwis, C.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase large chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2153
Polymers99,6731
Non-polymers5432
Water4,378243
1
A: Ribonucleoside-diphosphate reductase large chain 1
hetero molecules

A: Ribonucleoside-diphosphate reductase large chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,4316
Polymers199,3462
Non-polymers1,0854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4410 Å2
ΔGint-41 kcal/mol
Surface area43930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.353, 118.208, 63.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-899-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase large chain 1 / Ribonucleotide reductase R1 subunit 1 / Ribonucleotide reductase large subunit 1


Mass: 99672.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNR1, CRT7, RIR1, SDS12, YER070W / Production host: Escherichia coli (E. coli)
References: UniProt: P21524, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-N5P / 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO-1H-INDOLE / 5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE


Mass: 518.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O14P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mg/mL protein, 0.1 M sodium acetate at pH 6.5, 25% PEG 3350, 0.2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 37126 / Num. obs: 37089 / % possible obs: 99.9 % / Observed criterion σ(F): 3.5 / Observed criterion σ(I): 3.5
Reflection shellHighest resolution: 2.3 Å / Redundancy: 5.7 % / Rsym value: 0.496 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.969 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 1860 5.01 %RANDOm
Rwork0.1882 ---
all0.1904 36133 --
obs0.1882 37089 99.96 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.749 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5061 Å2-0 Å20 Å2
2---12.0005 Å20 Å2
3---14.5066 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 33 243 5070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084938
X-RAY DIFFRACTIONf_angle_d1.3036706
X-RAY DIFFRACTIONf_dihedral_angle_d16.6761788
X-RAY DIFFRACTIONf_chiral_restr0.093743
X-RAY DIFFRACTIONf_plane_restr0.006852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36220.27931560.21192661X-RAY DIFFRACTION100
2.3622-2.43160.27541350.20822660X-RAY DIFFRACTION100
2.4316-2.510.30451500.21072647X-RAY DIFFRACTION100
2.51-2.59950.25491570.20042676X-RAY DIFFRACTION100
2.5995-2.70330.25081520.19742667X-RAY DIFFRACTION100
2.7033-2.8260.23021380.19252690X-RAY DIFFRACTION100
2.826-2.97460.27391280.2032716X-RAY DIFFRACTION100
2.9746-3.16030.2771480.20132689X-RAY DIFFRACTION100
3.1603-3.40320.25051090.19222758X-RAY DIFFRACTION100
3.4032-3.74360.20681480.17652714X-RAY DIFFRACTION100
3.7436-4.28070.20471320.16842743X-RAY DIFFRACTION100
4.2807-5.37570.20451590.16472774X-RAY DIFFRACTION100
5.3757-19.96930.22421480.20342878X-RAY DIFFRACTION100

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