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- PDB-6m9m: Streptococcus mutans AlkD2 bound to inosine-5'-monophosphate -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6m9m
TitleStreptococcus mutans AlkD2 bound to inosine-5'-monophosphate
ComponentsAlkD2
KeywordsUNKNOWN FUNCTION / HEAT-like repeat / nucleotide binding
Function / homology
Function and homology information


Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #70 / ARM repeat domains / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
INOSINIC ACID / Phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsEichman, B.F. / Shi, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517695 United States
CitationJournal: Bioessays / Year: 2018
Title: Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases.
Authors: Shi, R. / Shen, X.X. / Rokas, A. / Eichman, B.F.
History
DepositionAug 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: AlkD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9673
Polymers24,5831
Non-polymers3842
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.152, 63.041, 65.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AlkD2


Mass: 24583.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: ALKD2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL00
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 18% (w/v) PEG 3350, 200 mM sodium phosphate, pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 49016 / % possible obs: 98.5 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Χ2: 1.048 / Net I/σ(I): 14 / Num. measured all: 691091
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.4512.80.33348230.9730.0960.3470.70798.8
1.45-1.5114.60.24748760.9890.0660.2560.75199.1
1.51-1.5814.70.17548800.9940.0470.1820.79399.2
1.58-1.6614.70.13348710.9960.0360.1380.83299.5
1.66-1.7614.70.10549070.9970.0280.1090.99699.7
1.76-1.914.50.08649480.9980.0230.0891.30699.6
1.9-2.0913.70.06449260.9990.0180.0661.45799.2
2.09-2.3913.40.05246370.9990.0140.0541.33793
2.39-3.0214.70.04450570.9990.0120.0451.369100
3.02-5013.20.0350910.9990.0090.0320.92197

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X8Q

4x8q


Resolution: 1.401→28.407 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.74
RfactorNum. reflection% reflection
Rfree0.1729 1995 4.08 %
Rwork0.136 --
obs0.1375 48954 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.62 Å2 / Biso mean: 20.3897 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.401→28.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 35 438 2208
Biso mean--50.27 33.76 -
Num. residues----207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4005-1.43560.1951370.13393309344699
1.4356-1.47440.17241290.1193341347099
1.4744-1.51770.16181530.11133304345799
1.5177-1.56670.16321490.10573312346199
1.5667-1.62270.14031350.106233953530100
1.6227-1.68770.13141470.10193317346499
1.6877-1.76450.14481500.115633653515100
1.7645-1.85750.16311450.126733973542100
1.8575-1.97380.18881380.15213353349199
1.9738-2.12620.1831410.135534103551100
2.1262-2.34010.17451260.13553087321390
2.3401-2.67850.15061440.134934183562100
2.6785-3.37370.17031420.141934903632100
3.3737-28.41240.20031590.15483461362096

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