[English] 日本語
Yorodumi
- PDB-6ebz: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta S... -

+
Open data


ID or keywords:

Loading...

-
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 / membrane / metal ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THIOCYANATE ION / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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: F2I8X9, 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more