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- PDB-5ci3: Ribonucleotide reductase Y122 2,3,5-F3Y variant -

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Basic information

Entry
Database: PDB / ID: 5ci3
TitleRibonucleotide reductase Y122 2,3,5-F3Y variant
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / unnatural amino acid / fluorotyrosine / ferritin superfamily / metalloenzyme
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / 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
MU-OXO-DIIRON / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 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 area2460 Å2
ΔGint-129 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.216, 92.216, 207.044
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-403-

SO4

21A-516-

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(FY3)
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, 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: 3.2 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; 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 6M-F / Detector: PIXEL / Date: Jul 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: 2.4→50 Å / Num. all: 20961 / Num. obs: 20961 / % possible obs: 98.7 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.4 / % possible all: 91

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Processing

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

2alx


Resolution: 2.401→43.436 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 988 4.93 %
Rwork0.1659 --
obs0.1682 20042 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→43.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 23 209 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073029
X-RAY DIFFRACTIONf_angle_d0.8574119
X-RAY DIFFRACTIONf_dihedral_angle_d14.4051114
X-RAY DIFFRACTIONf_chiral_restr0.034448
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4007-2.52730.34721040.27352177X-RAY DIFFRACTION78
2.5273-2.68560.30221400.22562638X-RAY DIFFRACTION94
2.6856-2.89290.26631440.20262775X-RAY DIFFRACTION98
2.8929-3.18390.23651490.18922802X-RAY DIFFRACTION99
3.1839-3.64450.23581490.1642825X-RAY DIFFRACTION99
3.6445-4.59080.18661470.13632844X-RAY DIFFRACTION98
4.5908-43.44270.1951550.16532993X-RAY DIFFRACTION96
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)
11.22370.91980.20262.38791.15172.2779-0.01880.3422-0.31110.25420.5051-0.25860.41910.1135-0.42590.70460.1219-0.23520.7168-0.20220.6564-28.9545-31.6976-11.4434
21.31330.2079-0.91931.8631-0.35541.87040.21520.3883-0.29410.77220.528-1.20420.19451.1709-0.48880.87970.2646-0.50411.1364-0.57011.359-12.0203-36.3863-8.5586
31.51260.77110.31832.52020.00661.98610.087-0.0491-0.16541.25080.2927-0.7590.24930.3039-0.34061.15370.1915-0.31150.6981-0.20620.7876-23.1865-25.1772.6423
40.7369-0.7648-0.58331.70830.0490.80360.33430.1566-0.43451.0038-0.02790.13330.2161-0.117-0.37771.44280.2497-0.1741.0405-0.17980.8356-30.5993-23.15148.2637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 318 )
4X-RAY DIFFRACTION4chain 'A' and (resid 319 through 349 )

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