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- PDB-5ci4: Ribonucleotide reductase beta subunit -

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Basic information

Entry
Database: PDB / ID: 5ci4
TitleRibonucleotide reductase beta subunit
ComponentsRibonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein
KeywordsOXIDOREDUCTASE / 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 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
Similarity search - Component
Biological speciesEscherichia coli 1303 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)43,8435
Polymers43,4271
Non-polymers4164
Water3,801211
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)87,68510
Polymers86,8542
Non-polymers8328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7220 Å2
ΔGint-93 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.508, 91.508, 205.179
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-526-

HOH

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Components

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


Mass: 43426.863 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.86 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: 2.05→50 Å / Num. all: 31952 / Num. obs: 31952 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.1 / % possible all: 76.2

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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: 2.05→45.754 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1580 4.98 %
Rwork0.1875 --
obs0.1892 31746 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→45.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 18 211 3083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083005
X-RAY DIFFRACTIONf_angle_d0.9914083
X-RAY DIFFRACTIONf_dihedral_angle_d15.2711112
X-RAY DIFFRACTIONf_chiral_restr0.036447
X-RAY DIFFRACTIONf_plane_restr0.007529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.36651230.34462271X-RAY DIFFRACTION82
2.1162-2.19180.40541370.31452645X-RAY DIFFRACTION96
2.1918-2.27960.33751450.29292751X-RAY DIFFRACTION99
2.2796-2.38330.36111410.27592733X-RAY DIFFRACTION99
2.3833-2.5090.30971480.27022732X-RAY DIFFRACTION99
2.509-2.66620.30411390.24922785X-RAY DIFFRACTION99
2.6662-2.8720.29561480.24632777X-RAY DIFFRACTION99
2.872-3.16090.26581460.23072784X-RAY DIFFRACTION99
3.1609-3.61820.2271480.19162828X-RAY DIFFRACTION99
3.6182-4.55790.17311500.14642834X-RAY DIFFRACTION98
4.5579-45.76540.1761550.15263026X-RAY DIFFRACTION98
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)
12.77561.89081.32354.2458-0.32642.5820.27710.3382-0.80060.8240.3139-0.42811.13570.0446-0.4961.03040.2259-0.21540.5544-0.13220.6884-31.9706-49.4697-9.4373
23.8133.48650.82673.52751.17930.7734-0.8211.2050.3167-0.38381.33440.4487-0.35860.1372-0.53990.73220.00830.05410.67310.13710.6535-32.0406-11.5056-13.816
31.76642.03640.71564.54612.27721.9242-0.08910.5179-0.24130.63260.6361-0.47960.24710.4331-0.49880.56610.169-0.08880.6923-0.06670.5677-24.2213-26.2506-11.6998
41.3069-0.12240.2273.67870.01471.89030.02090.4895-0.42941.06590.7856-1.53070.30731.4801-0.31970.72830.5188-0.48070.9786-0.47851.1543-11.3624-36.3781-8.3911
51.91041.96820.56183.793-0.61152.52520.09970.1967-0.1171.28090.2077-0.01880.41980.2063-0.25760.69190.1756-0.0090.4242-0.0080.3556-28.8941-23.3568-1.7014
62.18460.8260.15615.5202-2.05952.21560.0057-0.0886-0.26021.22280.2098-0.85920.35170.5111-0.13831.24180.3352-0.39790.6668-0.17210.6996-17.5611-26.44486.2717
72.5205-2.4716-1.67144.98190.53011.4920.32340.1797-0.35471.03390.0499-0.00160.5112-0.1708-0.41011.38130.3782-0.11670.7646-0.0240.6757-29.9253-23.04898.4809
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 205 )
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 318 )
7X-RAY DIFFRACTION7chain 'A' and (resid 319 through 349 )

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