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- PDB-8dq5: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(... -

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Basic information

Entry
Database: PDB / ID: 8dq5
TitleX-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase T191I variant
ComponentsRibonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding / membrane
Similarity search - Function
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
: / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRose, H.R. / 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: To Be Published
Title: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase T191I variant
Authors: Rose, H.R. / Boal, A.K.
History
DepositionJul 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,0627
Polymers79,8182
Non-polymers2445
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-48 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.771, 53.771, 221.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Ribonucleoside-diphosphate reductase


Mass: 39909.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A5FCJ5, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.2 M Mg-acetate, 20% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36014 / % possible obs: 98.5 % / Redundancy: 5.5 % / CC1/2: 0.899 / Rpim(I) all: 0.042 / Net I/σ(I): 18.76
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1964 / CC1/2: 0.678 / Rpim(I) all: 0.387 / Rrim(I) all: 0.853 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CWP

6cwp


Resolution: 2.1→46.57 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 31.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 1816 5.04 %
Rwork0.2465 34198 -
obs0.2483 36014 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.12 Å2 / Biso mean: 30.5147 Å2 / Biso min: 2.98 Å2
Refinement stepCycle: final / Resolution: 2.1→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 5 57 4698
Biso mean--31.58 20.95 -
Num. residues----562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.2416430.2881068111134
2.16-2.220.4035680.27631555162351
2.22-2.290.2901950.26471930202564
2.29-2.370.34191350.27872576271184
2.38-2.470.32381690.28122897306695
2.47-2.580.3141580.26833020317898
2.58-2.720.31351770.27272922309998
2.72-2.890.32151560.26583019317599
2.89-3.110.30281550.26223040319599
3.11-3.420.32341600.245530403200100
3.43-3.920.24951730.228530473220100
3.92-4.940.25821410.211730703211100
4.94-46.570.22491860.231830143200100

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