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- PDB-8dq4: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(... -

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Basic information

Entry
Database: PDB / ID: 8dq4
TitleX-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase beta subunit K71R 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: 2.35 Å
AuthorsRose, H.R. / Maggiolo, A.O. / Jung, J.J. / 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 beta subunit K71R 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)80,2187
Polymers79,9062
Non-polymers3125
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-26 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.551, 53.551, 220.947
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: 39953.004 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M magnesium acetate, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 28885 / % possible obs: 98.25 % / Redundancy: 5.8 % / CC1/2: 0.978 / Rpim(I) all: 0.033 / Rrim(I) all: 0.081 / Net I/σ(I): 21
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1467 / CC1/2: 0.978 / CC star: 0.994 / Rpim(I) all: 0.097 / Rrim(I) all: 0.239 / % possible all: 98.9

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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: 2.35→28.84 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 1465 5.07 %
Rwork0.2272 27417 -
obs0.2296 28882 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.67 Å2 / Biso mean: 34.9761 Å2 / Biso min: 5.36 Å2
Refinement stepCycle: final / Resolution: 2.35→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 10 62 4790
Biso mean--32.84 25.83 -
Num. residues----572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.440.38531350.28052596273191
2.44-2.540.30871430.25862749289299
2.54-2.650.32681410.258628172958100
2.65-2.790.28511420.249927732915100
2.79-2.970.27581500.252427682918100
2.97-3.190.30771510.24422764291599
3.19-3.510.28431640.23472712287698
3.52-4.020.25141520.206627732925100
4.02-5.060.22831320.19322746287898
5.07-28.840.2541550.20762719287498

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