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- PDB-1zkd: X-Ray structure of the putative protein Q6N1P6 from Rhodopseudomo... -

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Basic information

Entry
Database: PDB / ID: 1zkd
TitleX-Ray structure of the putative protein Q6N1P6 from Rhodopseudomonas palustris at the resolution 2.1 A , Northeast Structural Genomics Consortium target RpR58
ComponentsDUF185
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / RpR58 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3300 / Protein arginine methyltransferase NDUFAF7 / Protein arginine methyltransferase NDUFAF7 superfamily / Putative S-adenosyl-L-methionine-dependent methyltransferase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Vaccinia Virus protein VP39 / Helix non-globular / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3300 / Protein arginine methyltransferase NDUFAF7 / Protein arginine methyltransferase NDUFAF7 superfamily / Putative S-adenosyl-L-methionine-dependent methyltransferase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Vaccinia Virus protein VP39 / Helix non-globular / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKuzin, A.P. / Yong, W. / Vorobiev, S.M. / Acton, T. / Ma, L. / Xiao, R. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the putative protein Q6N1P6 from Rhodopseudomonas palustris at the resolution 2.1 A , Northeast Structural Genomics Consortium target RpR58
Authors: Kuzin, A.P. / Yong, W. / Vorobiev, S.M. / Acton, T. / Ma, L. / Xiao, R. / Montelione, G. / Tong, L. / Hunt, J.F.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF185
B: DUF185


Theoretical massNumber of molelcules
Total (without water)85,6432
Polymers85,6432
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.795, 79.795, 247.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DUF185


Mass: 42821.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA4359 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q6N1P6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.68 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8.5
Details: 4m Ammonium Acetate, 0.1M Tris-HCl, pH 8.5, microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913, 0.97942, 0.96774
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.979421
30.967741
ReflectionResolution: 2.1→30 Å / Num. obs: 99268 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 15.3 Å2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→22.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 230090.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4673 4.9 %RANDOM
Rwork0.223 ---
obs0.223 94661 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3738 Å2 / ksol: 0.34957 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å22.23 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.1→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 0 271 5740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 666 5.2 %
Rwork0.218 12161 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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