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

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Basic information

Entry
Database: PDB / ID: 6ebp
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form
ComponentsRibonucleoside-diphosphate reductase, beta subunit
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / post-translational modification / PTM / DOPA / radical
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
ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 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 6, 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 1.5Oct 11, 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 / pdbx_initial_refinement_model / 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_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.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 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)163,33814
Polymers162,7304
Non-polymers60910
Water11,746652
1
A: Ribonucleoside-diphosphate reductase, beta subunit
B: Ribonucleoside-diphosphate reductase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7098
Polymers81,3652
Non-polymers3446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-56 kcal/mol
Surface area23190 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)81,6296
Polymers81,3652
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5730 Å2
ΔGint-57 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.004, 109.417, 83.861
Angle α, β, γ (deg.)90.000, 90.060, 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 / Mutation: Y123(DAH)
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS RESIDUE REPRESENTS A POST-TRANSLATIONAL MOFIFICATION

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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: 2.26 Å3/Da / Density % sol: 45.47 % / Mosaicity: 0.434 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% (w/v) PEG 4000, 0.3 M calcium chloride, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.544
11-h,-k,l20.456
ReflectionResolution: 1.59→50 Å / Num. obs: 193462 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.031 / Rrim(I) all: 0.086 / Χ2: 0.932 / Net I/σ(I): 8.5 / Num. measured all: 1407352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.59-1.626.70.89595220.7670.360.9660.77598.8
1.62-1.6570.76195640.8320.3020.8190.80198.8
1.65-1.6870.68495790.8550.270.7360.8198.9
1.68-1.7170.59595840.8850.2340.640.82898.8
1.71-1.7570.52295670.9030.2050.5610.8499.1
1.75-1.797.10.4596300.9290.1770.4840.85199.2
1.79-1.847.10.38296400.9530.150.4110.86899.5
1.84-1.897.10.33196140.9520.130.3560.90899.6
1.89-1.947.10.26696990.970.1040.2860.97299.8
1.94-27.10.21197270.9790.0830.2271.01499.9
2-2.077.20.17296440.9830.0680.1851.09699.9
2.07-2.167.30.13697660.9890.0530.1461.122100
2.16-2.267.30.11396270.9920.0440.1221.112100
2.26-2.387.40.09297150.9950.0360.0991.04100
2.38-2.527.60.07697270.9960.0290.0811.008100
2.52-2.727.70.06997150.9960.0270.0741.098100
2.72-2.997.70.0697280.9960.0230.0641.235100
2.99-3.437.70.04297550.9980.0160.0450.922100
3.43-4.327.70.03197930.9990.0120.0330.69100
4.32-507.60.0398660.9990.0110.0320.60199.8

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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
Starting model: 6EBO

6ebo


Resolution: 1.59→35.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.898 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.015
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 9236 5 %RANDOM
Rwork0.1628 ---
obs0.1637 175576 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 36.34 Å2 / Biso mean: 13.882 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0 Å2-0.81 Å2
2--0.65 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.59→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10023 0 30 652 10705
Biso mean--19.93 17.46 -
Num. residues----1229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210299
X-RAY DIFFRACTIONr_bond_other_d0.0010.029587
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.95513984
X-RAY DIFFRACTIONr_angle_other_deg0.893322038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.03151225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82124.761523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.204151715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7561547
X-RAY DIFFRACTIONr_chiral_restr0.0610.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022483
LS refinement shellResolution: 1.586→1.627 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 412 -
Rwork0.184 8694 -
all-9106 -
obs--63.32 %

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