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- PDB-6l3r: Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in... -

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Basic information

Entry
Database: PDB / ID: 6l3r
TitleCrystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 4-bromo-N-((1S,2R)-2-(naphthalen-1-yl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)benzenesulfonamide
ComponentsRibonucleoside-diphosphate reductase large subunit
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / response to ionizing radiation / DNA synthesis involved in DNA repair / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / cell projection / male gonad development / disordered domain specific binding / nuclear envelope / retina development in camera-type eye / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol
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, barrel domain
Similarity search - Domain/homology
ACETATE ION / Chem-E4X / THYMIDINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiyahara, S. / Chong, K.T. / Suzuki, T.
CitationJournal: To be published
Title: TAS1553, a novel small molecule ribonucleotide reductase (RNR) subunit interaction inhibitor, displays remarkable anti-tumor activity
Authors: Miyahara, S. / Hara, S. / Chong, K.T. / Suzuki, T. / Ogino, Y. / Hoshino, T. / Tsukioka, S. / Yano, W. / Suzuki, M. / Otsu, Y. / Yonekura, T. / Ito, S. / Terasaka, M. / Suzuki, T. / Hashimoto, A.
History
DepositionOct 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase large subunit
E: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,64312
Polymers152,3802
Non-polymers2,26310
Water5,819323
1
A: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3036
Polymers76,1901
Non-polymers1,1135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area24950 Å2
MethodPISA
2
E: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3406
Polymers76,1901
Non-polymers1,1505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.860, 108.400, 130.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AE

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


Mass: 76189.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRM1, RR1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23921, ribonucleoside-diphosphate reductase

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Non-polymers , 6 types, 333 molecules

#2: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-E4X / 4-bromo-N-((1S,2R)-2-(naphthalen-1-yl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)benzenesulfonamide


Mass: 488.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18BrN3O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate buffer, PEG3350, Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→83.28 Å / Num. all: 101127 / Num. obs: 101127 / % possible obs: 98.9 % / Redundancy: 5.9 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Rsym value: 0.093 / Net I/av σ(I): 6.2 / Net I/σ(I): 12.5 / Num. measured all: 591920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.115.40.3452.279096145470.1580.3810.3454.898.5
2.11-2.245.60.2652.877027137670.1190.2920.2656.398.4
2.24-2.395.70.2073.673114129330.0920.2280.2077.898.5
2.39-2.585.70.1614.568951121330.0710.1770.1619.398.6
2.58-2.835.80.1215.964493111900.0530.1330.12111.698.8
2.83-3.165.90.0947.159415101520.0410.1030.09414.998.9
3.16-3.6560.0748.35486290940.0320.0810.0742099.7
3.65-4.476.60.0619.95111177810.0250.0660.06125.6100
4.47-6.326.90.054104227060950.0220.0580.05425.5100
6.32-47.9256.30.04611.52158134350.020.050.04623.198.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA3.3.9data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WGH

2wgh


Resolution: 2→47.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.464 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.16
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 5058 5 %RANDOM
Rwork0.1892 ---
obs0.1914 96003 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.74 Å2 / Biso mean: 25.462 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10511 0 137 323 10971
Biso mean--39.42 22.91 -
Num. residues----1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910884
X-RAY DIFFRACTIONr_bond_other_d0.0060.029969
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.96914755
X-RAY DIFFRACTIONr_angle_other_deg1.063323180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29451307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23224.597496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.517151901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7881552
X-RAY DIFFRACTIONr_chiral_restr0.1130.21613
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211927
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022189
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 368 -
Rwork0.263 6976 -
all-7344 -
obs--98.04 %

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