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- PDB-5ci2: Ribonucleotide reductase Y122 2,3,6-F3Y variant -

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Basic information

Entry
Database: PDB / ID: 5ci2
TitleRibonucleotide reductase Y122 2,3,6-F3Y variant
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / unnatural amino acid / fluorotyrosine / ferritin superfamily / metalloenzyme
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / metal ion binding / identical protein binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / metal ion binding / identical protein binding / cytoplasm / 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
MU-OXO-DIIRON / Ribonucleoside-diphosphate reductase 1 subunit beta / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFunk, M.A. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)0645960 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example.
Authors: Oyala, P.H. / Ravichandran, K.R. / Funk, M.A. / Stucky, P.A. / Stich, T.A. / Drennan, C.L. / Britt, R.D. / Stubbe, J.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _struct_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9936
Polymers43,4811
Non-polymers5125
Water3,765209
1
A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,98612
Polymers86,9622
Non-polymers1,02410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2450 Å2
ΔGint-128 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.420, 91.420, 206.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase 1 subunit beta / Protein B2 / Protein R2 / Ribonucleotide reductase 1


Mass: 43480.832 Da / Num. of mol.: 1 / Mutation: Y122(F6Y)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: nrdB, ftsB, Z3491, ECs3118 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P69925, UniProt: P69924*PLUS, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 61 %
Description: large, three-dimensional, yellow-green hexagons
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 1.1 M (NH4)2SO4, 0.9-1.2 M KCl, and 0.1 M Tris pH 8.0; 1:1 protein to precipitant; crystals grow over 1-3 days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 25083 / Num. obs: 25083 / % possible obs: 99.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ALX

2alx


Resolution: 2.25→44.631 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1966 1239 4.96 %
Rwork0.1718 --
obs0.1731 24970 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→44.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 23 209 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052981
X-RAY DIFFRACTIONf_angle_d0.7384046
X-RAY DIFFRACTIONf_dihedral_angle_d14.2171093
X-RAY DIFFRACTIONf_chiral_restr0.03441
X-RAY DIFFRACTIONf_plane_restr0.003518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.34010.37721290.3282523X-RAY DIFFRACTION97
2.3401-2.44660.3151320.27232571X-RAY DIFFRACTION99
2.4466-2.57560.31751370.25042579X-RAY DIFFRACTION100
2.5756-2.73690.26991360.2292596X-RAY DIFFRACTION100
2.7369-2.94820.26591380.22712619X-RAY DIFFRACTION100
2.9482-3.24480.23651360.21012624X-RAY DIFFRACTION100
3.2448-3.71420.19561400.16882640X-RAY DIFFRACTION100
3.7142-4.67870.16171420.13522700X-RAY DIFFRACTION100
4.6787-44.63950.16671490.15212879X-RAY DIFFRACTION100
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)
11.25761.1771-1.03342.2880.10031.78180.11870.34290.57950.74020.23150.3971-0.58970.269200.87580.080.18340.55640.08090.73431.742149.3394-9.4676
20.4042-0.0852-0.32760.5198-0.1520.4807-0.38280.7745-0.108-0.66570.8481-0.47540.23270.0290.00010.96290.03690.01420.697-0.03720.711731.894411.8999-13.8696
31.84710.8008-0.13041.1286-1.30912.1064-0.06410.36420.07630.22740.36650.18810.0739-0.0866-00.64340.09010.12120.59670.06560.586624.176726.2434-11.5577
41.6020.2687-0.19992.6446-0.52751.58510.04140.17880.1620.6840.43891.0465-0.1721-0.55510.0990.64890.13560.27060.64320.21890.82814.731231.5749-6.9479
52.26081.6359-0.83071.2339-0.76451.03350.1080.02620.0950.76470.2356-0.04-0.13270.3102-0.00010.85930.10450.0280.52810.01590.488430.190529.8308-2.0978
61.53910.7526-0.52791.23790.59552.24850.0233-0.12750.09861.29670.14790.78880.0794-0.23020.0041.03970.15240.33820.56790.10330.744317.43526.21636.0482
71.5678-1.28540.87861.6458-0.14411.04020.1806-0.01650.38090.47280.1559-0.5035-0.32810.5316-0.00011.35710.2030.20680.82320.0530.836829.924723.03118.3894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 224 )
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 318 )
7X-RAY DIFFRACTION7chain 'A' and (resid 319 through 349 )

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