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

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Basic information

Entry
Database: PDB / ID: 6lkm
TitleCrystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 5-chloro-N-((1S,2R)-2-(6-fluoro-2,3-dimethylphenyl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)-4-methyl-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-sulfonamide
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 / 2'-deoxyribonucleotide biosynthetic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / response to ionizing radiation / DNA synthesis involved in DNA repair / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of G1/S transition of mitotic cell cycle / centriolar satellite / male gonad development / disordered domain specific binding / nuclear envelope / retina development in camera-type eye / ciliary basal body / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / 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
Chem-EJ6 / THYMIDINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionDec 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 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
B: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,4158
Polymers152,3802
Non-polymers2,0356
Water46826
1
A: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2074
Polymers76,1901
Non-polymers1,0173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-3 kcal/mol
Surface area25690 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2074
Polymers76,1901
Non-polymers1,0173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.830, 66.920, 110.000
Angle α, β, γ (deg.)90.000, 103.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Chemical ChemComp-EJ6 / 5-chloro-N-((1S,2R)-2-(6-fluoro-2,3-dimethylphenyl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)-4-methyl-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-sulfonamide


Mass: 510.966 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24ClFN4O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.68 Å3/Da / Density % sol: 54.07 % / Mosaicity: 0.56 °
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-1A / Wavelength: 0.997 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.55→110.617 Å / Num. obs: 52639 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.086 / Rsym value: 0.071 / Net I/av σ(I): 7.6 / Net I/σ(I): 10.1
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
2.55-2.692.70.3282.12065575660.2350.4060.3283.298.6
2.69-2.852.90.2322.82110372190.1620.2840.2324.599.5
2.85-3.052.90.1663.91958168220.1170.2040.166699.5
3.05-3.293.20.1164.82037563040.0770.140.1168.899.4
3.29-3.613.40.0837.71966158140.0530.0990.08311.999.4
3.61-4.033.30.06791727453010.0440.0810.06714.799.7
4.03-4.662.90.0599.41361647010.0410.0720.05916.1100
4.66-5.73.10.05210.51240940150.0350.0630.05216.6100
5.7-8.063.30.04312.71022531240.0280.0520.04317.4100
8.06-64.0543.40.0319.5599917730.0190.0350.0320.299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WGH

2wgh


Resolution: 2.55→110.617 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.404 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.665 / ESU R Free: 0.333
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 2605 5 %RANDOM
Rwork0.2102 ---
obs0.2135 50006 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.7 Å2 / Biso mean: 51.036 Å2 / Biso min: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.55→110.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10546 0 128 26 10700
Biso mean--57.76 38.54 -
Num. residues----1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910911
X-RAY DIFFRACTIONr_bond_other_d0.0060.029957
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.97114814
X-RAY DIFFRACTIONr_angle_other_deg1.05323127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08551330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86724.579487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.954151874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2951552
X-RAY DIFFRACTIONr_chiral_restr0.0880.21630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212034
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022178
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 216 -
Rwork0.325 3628 -
all-3844 -
obs--98.49 %

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