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- PDB-5ci0: Ribonucleotide reductase Y122 3,5-F2Y variant -

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Basic information

Entry
Database: PDB / ID: 5ci0
TitleRibonucleotide reductase Y122 3,5-F2Y variant
ComponentsRibonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein
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
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
Similarity search - Component
Biological speciesEscherichia coli 1303 (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 / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
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.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_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, beta subunit, ferritin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9756
Polymers43,4631
Non-polymers5125
Water3,783210
1
A: Ribonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein
hetero molecules

A: Ribonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,95012
Polymers86,9262
Non-polymers1,02410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7880 Å2
ΔGint-145 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.613, 91.613, 205.650
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-524-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein


Mass: 43462.840 Da / Num. of mol.: 1 / Mutation: Y122FY3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 1303 (bacteria) / Gene: nrdB, EC1303_c24130 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E1LZC3, 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.: 210 / 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; 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: Apr 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: 25037 / Num. obs: 25037 / % possible obs: 99.6 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 27.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.3 / % 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→45.806 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1248 5.01 %Random
Rwork0.1809 ---
obs0.1825 24894 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→45.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 23 210 3068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032942
X-RAY DIFFRACTIONf_angle_d0.6883988
X-RAY DIFFRACTIONf_dihedral_angle_d14.7221082
X-RAY DIFFRACTIONf_chiral_restr0.027437
X-RAY DIFFRACTIONf_plane_restr0.003511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2503-2.34040.32921310.30812498X-RAY DIFFRACTION96
2.3404-2.4470.29331360.26262547X-RAY DIFFRACTION99
2.447-2.5760.27061350.24182580X-RAY DIFFRACTION100
2.576-2.73730.23011370.22342592X-RAY DIFFRACTION100
2.7373-2.94860.29461380.22712602X-RAY DIFFRACTION100
2.9486-3.24530.24891380.21212616X-RAY DIFFRACTION100
3.2453-3.71470.22341390.18082645X-RAY DIFFRACTION100
3.7147-4.67940.17821420.14292701X-RAY DIFFRACTION100
4.6794-45.8160.17421520.15352865X-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)
11.25941.54890.48454.81191.51631.85020.09030.2405-0.22390.4190.2875-0.1740.52260.1151-0.29350.55220.153-0.09090.522-0.04450.4204-31.9053-37.2185-10.683
21.55830.82260.65232.78611.21792.43770.1190.3599-0.36720.61040.3701-0.75270.3730.7079-0.33620.46210.1924-0.15720.5978-0.16340.527-20.3402-29.5765-7.6989
31.60480.63360.31384.0714-0.69652.4480.09310.005-0.31460.98760.1564-0.81010.31270.4613-0.2040.83440.2034-0.29590.5687-0.13760.584-17.5852-26.58176.2369
42.7737-3.0932-1.57267.5977-0.64192.41410.23070.0014-0.25430.71050.15550.33830.2564-0.5139-0.39350.94850.2002-0.0780.6208-0.02690.5707-29.7813-22.22478.4533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 254 )
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 319 )
4X-RAY DIFFRACTION4chain 'A' and (resid 320 through 346 )

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