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- PDB-6ebz: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta S... -

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Basic information

Entry
Database: PDB / ID: 6ebz
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form with Thiocyanate Bound
ComponentsRibonucleoside-diphosphate reductase, beta subunit
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / post-translational modification / PTM / DOPA / radical / SCN / thiocyanate
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding / membrane
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / 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
THIOCYANATE ION / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsPalowitch, G.M. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119707 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.
Authors: Blaesi, E.J. / Palowitch, G.M. / Hu, K. / Kim, A.J. / Rose, H.R. / Alapati, R. / Lougee, M.G. / Kim, H.J. / Taguchi, A.T. / Tan, K.O. / Laremore, T.N. / Griffin, R.G. / Krebs, C. / Matthews, ...Authors: Blaesi, E.J. / Palowitch, G.M. / Hu, K. / Kim, A.J. / Rose, H.R. / Alapati, R. / Lougee, M.G. / Kim, H.J. / Taguchi, A.T. / Tan, K.O. / Laremore, T.N. / Griffin, R.G. / Krebs, C. / Matthews, M.L. / Silakov, A. / Bollinger Jr., J.M. / Allen, B.D. / Boal, A.K.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 30, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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
Revision 2.0Dec 24, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity_poly / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase, beta subunit
B: Ribonucleoside-diphosphate reductase, beta subunit
C: Ribonucleoside-diphosphate reductase, beta subunit
D: Ribonucleoside-diphosphate reductase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,44517
Polymers162,7304
Non-polymers71513
Water11,638646
1
A: Ribonucleoside-diphosphate reductase, beta subunit
B: Ribonucleoside-diphosphate reductase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,84310
Polymers81,3652
Non-polymers4798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-71 kcal/mol
Surface area22830 Å2
MethodPISA
2
C: Ribonucleoside-diphosphate reductase, beta subunit
hetero molecules

D: Ribonucleoside-diphosphate reductase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6017
Polymers81,3652
Non-polymers2365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6120 Å2
ΔGint-66 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.041, 108.973, 84.031
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonucleoside-diphosphate reductase, beta subunit


Mass: 40682.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus urinae (strain ACS-120-V-Col10a) (bacteria)
Strain: ACS-120-V-Col10a / Gene: HMPREF9243_0731 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A178HFF8, UniProt: F2I8X9*PLUS, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS RESIDUE REPRESENTS A POST-TRANSLATIONAL MODIFICATION

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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: 2.25 Å3/Da / Density % sol: 45.38 % / Mosaicity: 0.818 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 0.2 M calcium chloride, 0.15 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.733
11-h,-k,l20.267
ReflectionResolution: 1.66→50 Å / Num. obs: 163766 / % possible obs: 96.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.043 / Rrim(I) all: 0.095 / Χ2: 0.894 / Net I/σ(I): 8.7 / Num. measured all: 632884
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.66-1.692.10.82367980.4480.5921.0210.76980.9
1.69-1.722.40.81676430.4750.5570.9960.77590.3
1.72-1.752.90.77180730.5710.4810.9150.76795.3
1.75-1.793.40.72382650.6930.4210.8420.77696.8
1.79-1.833.80.6681650.7510.3670.7590.78897
1.83-1.8740.59183140.7890.3210.6750.7998
1.87-1.9240.47582640.8630.2560.5420.81297.9
1.92-1.9740.39282950.90.2110.4480.8398.1
1.97-2.033.90.29283070.9190.1610.3350.84298.4
2.03-2.0940.22983890.9480.1250.2620.87298.6
2.09-2.174.10.17983370.9630.0960.2040.90498.5
2.17-2.254.10.15283580.9690.0810.1730.95198.3
2.25-2.364.20.12683030.9780.0650.1430.95298.1
2.36-2.484.10.10883400.9810.0550.1220.96198
2.48-2.634.10.0982910.9840.0470.1020.94697.7
2.63-2.843.90.07782430.9860.040.0870.9996.8
2.84-3.124.10.06983030.9860.0350.0780.99697.4
3.12-3.584.50.06583530.9920.0310.0721.04898.3
3.58-4.54.50.0682450.9910.0290.0670.99396.3
4.5-504.50.05484800.9890.0270.0610.84397.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→45.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.686 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7504 5.1 %RANDOM
Rwork0.1957 ---
obs0.1967 140309 86.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 48.2 Å2 / Biso mean: 15.62 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å2-0 Å2-1.27 Å2
2--2.31 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.66→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10035 0 33 646 10714
Biso mean--27.33 19.22 -
Num. residues----1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210358
X-RAY DIFFRACTIONr_bond_other_d0.0010.029619
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.95414067
X-RAY DIFFRACTIONr_angle_other_deg0.891322123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.97451238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53624.791526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.549151726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2651546
X-RAY DIFFRACTIONr_chiral_restr0.0580.21514
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022502
LS refinement shellResolution: 1.656→1.699 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 221 -
Rwork0.33 3950 -
all-4171 -
obs--33.07 %

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