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- PDB-3e23: Crystal structure of the RPA2492 protein in complex with SAM from... -

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Basic information

Entry
Database: PDB / ID: 3.0E+23
TitleCrystal structure of the RPA2492 protein in complex with SAM from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR299
Componentsuncharacterized protein RPA2492
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function
Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Methyltransferase type 11 domain-containing protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsForouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Tong, S. / Everett, J.K. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the RPA2492 protein in complex with SAM from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR299
Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Tong, S. / K Everett, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein RPA2492
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6367
Polymers23,7571
Non-polymers8796
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.185, 65.295, 67.109
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 uncharacterized protein RPA2492


Mass: 23756.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA2492 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6N6X2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 277 K / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, and 5 mM S-adenosyl-methionine. Resevoir solution: 100 mM HEPES (pH 7.5) and 2 M ammonium sulfate. , microbatch under ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, and 5 mM S-adenosyl-methionine. Resevoir solution: 100 mM HEPES (pH 7.5) and 2 M ammonium sulfate. , microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97902 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 60048 / Num. obs: 54164 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.057 / Net I/σ(I): 33.94
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 12.77 / Num. unique all: 6000 / Rsym value: 0.109 / % possible all: 66.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 465336.69 / Data cutoff low absF: 2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.183 5207 9.7 %RANDOM
Rwork0.16 ---
all0.161 59601 --
obs0.16 53939 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9086 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---0.41 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 52 317 1915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.198 382 9.5 %
Rwork0.161 3635 -
obs-3635 67.2 %

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