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- PDB-5d1y: Low resolution crystal structure of human ribonucleotide reductas... -

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Basic information

Entry
Database: PDB / ID: 5d1y
TitleLow resolution crystal structure of human ribonucleotide reductase alpha6 hexamer in complex with dATP
ComponentsRibonucleoside-diphosphate reductase large subunitRibonucleotide reductase
KeywordsOXIDOREDUCTASE / deoxyribonucleotide / oligomerization / ATP cone
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / positive regulation of G0 to G1 transition / mitochondrial DNA replication / ribonucleoside diphosphate metabolic process / 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 / positive regulation of G0 to G1 transition / mitochondrial DNA replication / ribonucleoside diphosphate metabolic process / 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 / retina development in camera-type eye / nuclear envelope / 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
Ribonucleoside-diphosphate reductase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 9.005 Å
Model detailsThis structure has undergone only rigid body and group B-factor refinement. The data-to-parameter ...This structure has undergone only rigid body and group B-factor refinement. The data-to-parameter ratio (3405 reflections, 11559 atoms) was not sufficient for individual atom position or B-factor refinement.
AuthorsAndo, N. / Li, H. / Brignole, E.J. / Thompson, S. / McLaughlin, M.I. / Page, J. / Asturias, F. / Stubbe, J. / Drennan, C.L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-0936384 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM100008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM100008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29595 United States
CitationJournal: Biochemistry / Year: 2016
Title: Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer.
Authors: Ando, N. / Li, H. / Brignole, E.J. / Thompson, S. / McLaughlin, M.I. / Page, J.E. / Asturias, F.J. / Stubbe, J. / Drennan, C.L.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Nov 22, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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


Theoretical massNumber of molelcules
Total (without water)184,7012
Polymers184,7012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-11 kcal/mol
Surface area53030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)356.010, 356.010, 356.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase / Ribonucleoside-diphosphate reductase subunit M1 / Ribonucleotide reductase large subunit


Mass: 92350.391 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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P23921, ribonucleoside-diphosphate reductase

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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: 10.3 Å3/Da / Density % sol: 88 % / Description: hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES, 32% v/v Jeffamine M600, 10 mM DTT / PH range: 7 / Temp details: temperature-controlled room 292-294 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2011
Details: WHITE BEAM COLLIMATING MIRROR, VERTICALLY FOCUSING Rh-COATED Si MIRROR, HORIZONTALLY FOCUSING MONOCHROMATOR
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 9→79.861 Å / Num. obs: 6141 / % possible obs: 99.8 % / Redundancy: 15.7 % / Biso Wilson estimate: 50.01 Å2 / Rmerge(I) obs: 0.274 / Χ2: 1.014 / Net I/σ(I): 6.9 / Num. measured all: 50847
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
9-10.116.51.9621.73221.013100
11.39-11.85150.4443401.008100
11.85-12.3815.50.4083181.02100
12.38-13.0315.50.3433341.027100
13.03-13.8515.30.3053361.02100
13.85-14.9114.70.273391.02100
14.91-16.414.60.2213371.007100
16.4-18.74150.1853530.998100
18.74-23.52150.1413551.031100
23.52-8013.20.0823920.99198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
XDSdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HNC

3hnc


Resolution: 9.005→75.902 Å / SU ML: 1.74 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 50.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.4258 612 10.02 %Random selection
Rwork0.4054 5498 --
obs0.4074 6110 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 660.46 Å2 / Biso mean: 633.0471 Å2 / Biso min: 630.85 Å2
Refinement stepCycle: final / Resolution: 9.005→75.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11328 0 0 0 11328
Num. residues----1452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.10111577
X-RAY DIFFRACTIONf_angle_d1.51215743
X-RAY DIFFRACTIONf_chiral_restr0.0961783
X-RAY DIFFRACTIONf_plane_restr0.0092008
X-RAY DIFFRACTIONf_dihedral_angle_d20.8964158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
9.005-9.90940.43951480.416913301478
9.9094-11.33920.37721500.397313381488
11.3392-14.27070.44721510.400613651516
14.2707-75.90420.42961630.407514651628

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