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- PDB-9dws: X-ray crystal structure of Francisella hispaniensis apo ribonucle... -

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Basic information

Entry
Database: PDB / ID: 9dws
TitleX-ray crystal structure of Francisella hispaniensis apo ribonucleotide reductase beta subunit
Componentsribonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / diiron / tyrosyl radical / ferritin / four-helix bundle
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / cell redox homeostasis
Similarity search - Function
Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesFrancisella hispaniensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPeduzzi, O.M. / Lin, C.-Y. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2025
Title: A Structurally Divergent Class Ia Ribonucleotide Reductase from a Tick-Borne Pathogen.
Authors: Peduzzi, O.M. / Palowitch, G.M. / Gajewski, J.P. / Hu, K. / Wheeler, A. / Laremore, T.N. / Silletti, S. / Komives, E.A. / Allen, B.D. / Silakov, A. / Krebs, C. / Bollinger Jr., J.M. / Lin, C.Y. / Boal, A.K.
History
DepositionOct 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribonucleoside-diphosphate reductase
B: ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0583
Polymers76,0222
Non-polymers351
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-20 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.670, 98.030, 100.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ribonucleoside-diphosphate reductase


Mass: 38011.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella hispaniensis (bacteria) / Gene: FN3523_1088 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F4BFZ7, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8.5% (w/v) PEG 4000, 0.8 M lithium chloride, and 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→44.05 Å / Num. obs: 36537 / % possible obs: 99.93 % / Redundancy: 14.8 % / Biso Wilson estimate: 42.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1496 / Rpim(I) all: 0.04012 / Rrim(I) all: 0.155 / Net I/σ(I): 13.78
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 3612 / CC1/2: 0.705 / Rpim(I) all: 0.4561 / Rrim(I) all: 0.155 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.05 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 1822 4.99 %
Rwork0.171 --
obs0.1729 36527 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 1 195 4952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054886
X-RAY DIFFRACTIONf_angle_d0.7866603
X-RAY DIFFRACTIONf_dihedral_angle_d4.238634
X-RAY DIFFRACTIONf_chiral_restr0.046712
X-RAY DIFFRACTIONf_plane_restr0.005843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.28121330.24642632X-RAY DIFFRACTION100
2.36-2.430.27811430.22392627X-RAY DIFFRACTION100
2.43-2.510.27531410.21992649X-RAY DIFFRACTION100
2.51-2.60.24981380.20532619X-RAY DIFFRACTION100
2.6-2.70.23561400.1942657X-RAY DIFFRACTION100
2.7-2.830.24331440.19662627X-RAY DIFFRACTION100
2.83-2.980.24361410.20412654X-RAY DIFFRACTION100
2.98-3.160.26131350.20772643X-RAY DIFFRACTION100
3.16-3.410.23271360.18672675X-RAY DIFFRACTION100
3.41-3.750.20351360.16592668X-RAY DIFFRACTION100
3.75-4.290.19161400.13732698X-RAY DIFFRACTION100
4.29-5.40.16591450.13712731X-RAY DIFFRACTION100
5.41-44.050.16991500.15382825X-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)
12.06010.43180.07224.32591.15863.44250.69470.414-1.00190.22750.1275-0.81041.23080.6373-0.58640.67350.1192-0.24890.4513-0.09060.7691-4.7043.704-20.585
22.4503-0.95580.56824.89821.20972.80350.2461-0.0466-0.3485-0.1062-0.02280.7630.1273-0.458-0.1580.3112-0.00110.01560.35550.03260.4151-20.25520.812-20.277
33.2234-0.08361.24685.11831.43564.501-0.0514-0.15280.77140.0625-0.02850.6651-0.7946-0.57750.13930.52690.06710.10610.42840.04970.531-22.72346.372-13.782
43.5317-1.25710.19573.377-0.53443.08170.1619-0.070.08540.14770.1217-0.3008-0.09720.1137-0.30230.3245-0.0180.00090.3052-0.04070.2846-8.59324.65-20.483
52.8953-0.86220.69052.93951.16820.919-0.02970.18340.70340.0802-0.0346-0.9409-0.07310.09410.150.485-0.06140.13840.40650.05230.5356-2.39938.695-11.157
64.7975-0.68561.18722.5628-0.47184.67280.62650.17010.0232-0.521-0.269-0.34090.20560.2059-0.17880.3822-0.0602-0.02750.32130.0220.2957-0.95521.484-7.944
72.5136-1.13660.57051.8148-0.47592.7750.2642-0.1273-0.03790.1594-0.03830.11580.0215-0.2867-0.23320.3272-0.04010.04830.3350.03660.3564-17.3227.292-9.732
83.3563-2.11740.20885.8886-0.01442.4137-0.0959-0.70330.1410.7080.3501-0.1325-0.1359-0.1749-0.26570.4559-0.076-0.00730.4499-0.0110.2916-8.31629.8890.977
93.998-2.26680.7912.2955-0.00070.75970.0589-1.0151-0.56340.52560.34460.5813-0.1254-0.4268-0.56950.5296-0.04110.06840.65590.18020.4968-19.13725.942.72
101.9205-0.0428-0.32334.15521.66792.87010.22560.09-0.2044-0.0294-0.22080.41470.0718-0.2417-0.07640.28760.0611-0.06370.37840.02090.3484-17.16414.359-34.701
112.75380.89390.0573.97490.81062.87770.23940.1256-0.2597-0.14130.0742-0.15540.0670.1883-0.30350.2980.0416-0.03070.3485-0.0510.3354-8.12816.309-30.397
122.6799-0.13220.77621.87721.41151.43630.1488-0.1451-0.7343-0.12570.0089-0.59980.11050.4205-0.15530.55130.1203-0.07950.5521-0.09590.7123-1.6252.491-39.018
133.13751.1027-0.20183.83210.68173.0330.09770.5212-0.2952-0.75220.0784-0.0852-0.06240.1198-0.1850.43760.0851-0.03990.4681-0.08120.3278-8.63113.912-46.808
143.13941.14850.58321.46971.27741.77460.27850.79770.253-0.78820.19130.3844-0.357-0.4334-0.32470.75160.0781-0.12910.84460.04220.5053-15.15217.139-54.616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:22 )A9 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:44 )A23 - 44
3X-RAY DIFFRACTION3( CHAIN A AND RESID 45:73 )A45 - 73
4X-RAY DIFFRACTION4( CHAIN A AND RESID 74:119 )A74 - 119
5X-RAY DIFFRACTION5( CHAIN A AND RESID 120:150 )A120 - 150
6X-RAY DIFFRACTION6( CHAIN A AND RESID 151:166 )A151 - 166
7X-RAY DIFFRACTION7( CHAIN A AND RESID 167:216 )A167 - 216
8X-RAY DIFFRACTION8( CHAIN A AND RESID 217:276 )A217 - 276
9X-RAY DIFFRACTION9( CHAIN A AND RESID 277:297 )A277 - 297
10X-RAY DIFFRACTION10( CHAIN B AND RESID 8:72 )B8 - 72
11X-RAY DIFFRACTION11( CHAIN B AND RESID 73:119 )B73 - 119
12X-RAY DIFFRACTION12( CHAIN B AND RESID 120:150 )B120 - 150
13X-RAY DIFFRACTION13( CHAIN B AND RESID 151:275 )B151 - 275
14X-RAY DIFFRACTION14( CHAIN B AND RESID 276:297 )B276 - 297

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