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- PDB-2vux: Human ribonucleotide reductase, subunit M2 B -

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Basic information

Entry
Database: PDB / ID: 2vux
TitleHuman ribonucleotide reductase, subunit M2 B
ComponentsRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 B
KeywordsOXIDOREDUCTASE / DNA REPLICATION / DE NOVO PATHWAY / NUCLEOTIDE METABOLISM / RIBONUCLEOTIDE REDUCTASE / RNR / IRON / P53R2 / CASP8 / NUCLEUS / METAL-BINDING / DNA DAMAGE / DNA REPAIR / IRON BINDING / SUBUNIT M2 B
Function / homology
Function and homology information


deoxyribonucleoside triphosphate metabolic process / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / renal system process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase ...deoxyribonucleoside triphosphate metabolic process / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / renal system process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA synthesis involved in DNA repair / response to amine / positive regulation of G2/M transition of mitotic cell cycle / kidney development / TP53 Regulates Metabolic Genes / response to oxidative stress / DNA repair / mitochondrion / nucleoplasm / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ribonucleoside-diphosphate reductase subunit M2 B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWelin, M. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Welin, M. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Ribonucleotide Reductase, Subunit M2 B
Authors: Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. ...Authors: Welin, M. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Nordlund, P.
History
DepositionMay 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 B
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0404
Polymers75,9292
Non-polymers1122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-14.2 kcal/mol
Surface area28680 Å2
MethodPQS
Unit cell
Length a, b, c (Å)68.960, 99.470, 132.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5922, -0.2818, 0.7549), (-0.2746, -0.9514, -0.1398), (0.7575, -0.1245, -0.6408)
Vector: 16.23, -38.42, -48.7)

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Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 B / TP53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE M2 B / P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT ...TP53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE M2 B / P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2-LIKE PROTEIN / P53R2


Mass: 37964.379 Da / Num. of mol.: 2 / Fragment: RESIDUES 20-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7LG56, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
Sequence detailsPROTEIN WAS CO-CRYSTALLIZED IN THE PRESENCE OF CHYMOTRYPSIN.

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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: 3.2 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M NACACODYLATE PH 6.5, 2.3M AMMONIUM SULFATE, 0.2M SODIUM CHLORIDE. CHYMOTRYPSIN WAS ADDED TO A RATIO CHYMOTRYPSIN:PROTEIN OF 1:100 PRIOR TO CRYSTALLISATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2008 / Details: MIRRORS
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 22880 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.59 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.99
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.81 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UW2

2uw2


Resolution: 2.8→19.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / SU B: 30.141 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.662 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 38-42, 100-105 IN SUBUNIT A AND 38REMARK
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1831 8 %RANDOM
Rwork0.209 ---
obs0.213 21049 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 2 0 4362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224471
X-RAY DIFFRACTIONr_bond_other_d0.0010.023125
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.956028
X-RAY DIFFRACTIONr_angle_other_deg0.83737565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72123.929224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69115792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8941525
X-RAY DIFFRACTIONr_chiral_restr0.0610.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02986
X-RAY DIFFRACTIONr_nbd_refined0.2140.21090
X-RAY DIFFRACTIONr_nbd_other0.1730.23052
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22215
X-RAY DIFFRACTIONr_nbtor_other0.0870.22251
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5451.53409
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64124242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.93532228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4454.51786
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 133
Rwork0.284 1530
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)
11.9447-0.1064-1.41451.5059-0.64763.47710.11610.12270.161-0.03310.04230.1474-0.2728-0.2482-0.1584-0.18280.0192-0.0006-0.1948-0.0017-0.137222.2122-11.9514-1.9935
21.69980.3178-1.35221.85890.6083.5876-0.10.57530.0061-0.1419-0.06990.35230.0671-0.75410.1699-0.1187-0.0234-0.0067-0.0344-0.0558-0.076732.2762-33.3256-28.0706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 312
2X-RAY DIFFRACTION1A1313
3X-RAY DIFFRACTION2B31 - 314
4X-RAY DIFFRACTION2B1315

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