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- PDB-3mer: Crystal Structure of the methyltransferase Slr1183 from Synechocy... -

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Basic information

Entry
Database: PDB / ID: 3mer
TitleCrystal Structure of the methyltransferase Slr1183 from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR145
ComponentsSlr1183 protein
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Slr1183 protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeetharaman, J. / Chen, Y. / Forouhar, F. / Rossi, P. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / Everett, J.K. ...Seetharaman, J. / Chen, Y. / Forouhar, F. / Rossi, P. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target SgR145
Authors: Seetharaman, J. / Chen, Y. / Forouhar, F. / Rossi, P. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, ...Authors: Seetharaman, J. / Chen, Y. / Forouhar, F. / Rossi, P. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Slr1183 protein
B: Slr1183 protein


Theoretical massNumber of molelcules
Total (without water)44,8072
Polymers44,8072
Non-polymers00
Water1,08160
1
A: Slr1183 protein


Theoretical massNumber of molelcules
Total (without water)22,4031
Polymers22,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Slr1183 protein


Theoretical massNumber of molelcules
Total (without water)22,4031
Polymers22,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.440, 53.792, 53.845
Angle α, β, γ (deg.)115.490, 95.660, 84.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Slr1183 protein


Mass: 22403.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: slr1183 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P74712
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: microbatch, under oil / pH: 4
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Sodium Malonate (pH 4.0) and 12% PEG 3350. , Microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.00684 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00684 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 21262 / Num. obs: 20859 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.037 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2113 / Rsym value: 0.163 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i6g and 2kw5

2i6g

2kw5


Resolution: 2.2→19.61 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 535378.312 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 863 4.8 %RANDOM
Rwork0.224 ---
all0.228 21144 --
obs0.226 17804 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.726 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.85 Å2-0.71 Å2-2.11 Å2
2---5.7 Å214.18 Å2
3---10.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 0 60 2716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.32 62 4.7 %
Rwork0.309 1248 -
obs-1310 62.1 %

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