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- PDB-8dq3: X-ray crystal structure of Aggregatibacter actinomycetemcomitans ... -

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Basic information

Entry
Database: PDB / ID: 8dq3
TitleX-ray crystal structure of Aggregatibacter actinomycetemcomitans dimanganese(II) class Id ribonucleotide reductase beta subunit
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
FORMIC ACID / : / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRose, H.R. / 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 Aggregatibacter actinomycetemcomitans dimanganese(II) class Id ribonucleotide reductase beta subunit
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
C: Ribonucleoside-diphosphate reductase
D: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,52222
Polymers163,6614
Non-polymers86118
Water10,539585
1
A: Ribonucleoside-diphosphate reductase
B: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,29912
Polymers81,8312
Non-polymers46910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribonucleoside-diphosphate reductase
D: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,22310
Polymers81,8312
Non-polymers3928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.213, 156.540, 80.722
Angle α, β, γ (deg.)90.000, 91.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ribonucleoside-diphosphate reductase


Mass: 40915.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: FXB68_03595 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A142G3G1, ribonucleoside-diphosphate reductase

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Non-polymers , 5 types, 603 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.2 M magnesium formate, 16% (w/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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.67→44.22 Å / Num. obs: 148843 / % possible obs: 99.55 % / Redundancy: 7.4 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 27.235
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 14355 / CC1/2: 0.876 / CC star: 0.966 / % possible all: 100

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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: 7M8G

7m8g
PDB Unreleased entry


Resolution: 1.67→44.22 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 7460 5.01 %
Rwork0.1696 141370 -
obs0.1709 148830 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.38 Å2 / Biso mean: 15.7885 Å2 / Biso min: 4.03 Å2
Refinement stepCycle: final / Resolution: 1.67→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9905 0 33 585 10523
Biso mean--21.89 22.42 -
Num. residues----1185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.690.25282030.21094137434087
1.69-1.710.2562480.196846724920100
1.71-1.730.20482510.186347615012100
1.73-1.750.22462410.184646964937100
1.75-1.770.21942590.187647384997100
1.77-1.80.2232660.182747605026100
1.8-1.820.21492480.177646694917100
1.82-1.850.2042440.176647384982100
1.85-1.880.21622650.176146904955100
1.88-1.910.2342560.180847144970100
1.91-1.940.19232420.167147895031100
1.94-1.980.19222480.166747044952100
1.98-2.020.20512310.167247624993100
2.02-2.060.2272680.178746974965100
2.06-2.10.20092750.171346964971100
2.1-2.150.18822290.164247384967100
2.15-2.210.19212310.158647544985100
2.21-2.270.18532780.16647425020100
2.27-2.330.18672390.172846754914100
2.33-2.410.21472460.173447424988100
2.41-2.490.20552630.173847395002100
2.49-2.590.20352560.174447154971100
2.59-2.710.20212340.177647484982100
2.71-2.850.19442710.178946944965100
2.85-3.030.20922640.178947304994100
3.03-3.270.17422470.177647715018100
3.27-3.60.18732380.175747254963100
3.6-4.120.18642330.153647795012100
4.12-5.190.1682590.140847635022100
5.19-44.220.15382270.157848325059100

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