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- PDB-4g67: Crystal structure of a COG1565 superfamily member and likely meth... -

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Basic information

Entry
Database: PDB / ID: 4g67
TitleCrystal structure of a COG1565 superfamily member and likely methyl transferase from Burkholderia thailandensis bound to S-adenosyl-homocysteine
ComponentsUncharacterized ACR, COG1565 superfamily
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / methyltransferase superfamily / S-adenosyl methionine / SAM / AdoMet / SAH / AdoHcy / natural inhibitor / candidate essential gene
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
Rossmann fold - #12710 / Protein arginine methyltransferase NDUFAF7 / Protein arginine methyltransferase NDUFAF7 superfamily / Putative S-adenosyl-L-methionine-dependent methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized ACR, COG1565 superfamily
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ACR, COG1565 superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8076
Polymers46,1071
Non-polymers7015
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.630, 74.550, 111.790
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 Uncharacterized ACR, COG1565 superfamily


Mass: 46106.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH I0294, BTH_I0294 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T1U7
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: ButhA.17973.a.A1 PS01383 at 20 mg/mL with 2 mM SAH against JCSG+ H7 focus screen, 0.2 M ammonium sulfate, 0.1 M BisTris, 18% PEG 3350 and 15% ethylene glycol as cryo-protectant, crystal ...Details: ButhA.17973.a.A1 PS01383 at 20 mg/mL with 2 mM SAH against JCSG+ H7 focus screen, 0.2 M ammonium sulfate, 0.1 M BisTris, 18% PEG 3350 and 15% ethylene glycol as cryo-protectant, crystal tracking ID 234263h3, unique puck ID xgv5-2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 35828 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.529 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.5222.549752239791.2
1.85-1.90.4163.5612128254898.2
1.9-1.950.3774.5914255247299.7
1.95-2.010.3065.6214273242999.9
2.01-2.080.2427.1114189238999.9
2.08-2.150.2038.4313453223999.7
2.15-2.230.1829.54132502204100
2.23-2.320.15111.0812685211799.8
2.32-2.430.14111.6512371205599.9
2.43-2.550.11514.1811785195899.8
2.55-2.680.10714.7111271187499.7
2.68-2.850.09217.0210471175099.9
2.85-3.040.07919.299898167399.9
3.04-3.290.06621.639058155599.7
3.29-3.60.054268144142199.8
3.6-4.030.04828.657325131499.8
4.03-4.650.04331.796366117299.2
4.65-5.690.04430.47532799699.4
5.69-8.050.04229.45437079499.5
8.050.03233.86234947199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.63 Å
Translation3 Å45.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.76 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.269 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1783 5 %RANDOM
Rwork0.1586 ---
obs0.1605 35827 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.55 Å2 / Biso mean: 16.5289 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20 Å2
2---1.01 Å2-0 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 44 365 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193020
X-RAY DIFFRACTIONr_bond_other_d0.0010.022820
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9684114
X-RAY DIFFRACTIONr_angle_other_deg0.81836442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39522.256133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41915429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2181529
X-RAY DIFFRACTIONr_chiral_restr0.0860.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 106 -
Rwork0.238 2285 -
all-2391 -
obs--91.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2018-0.15220.06410.23670.05290.3873-0.02160.02950.04240.0211-0.00960.00140.03650.02010.03110.02670.0013-0.00640.02410.00110.043828.8506-5.4201-30.0043
20.75240.1094-0.03230.5618-0.07230.271-0.0128-0.06590.01530.06260.0147-0.04180.0057-0.0104-0.00190.05030.009-0.00840.04050.00810.008314.0669-9.2635-7.9248
30.951-0.3663-0.21050.14460.11510.40360.03810.1231-0.0366-0.0057-0.04210.01420.09050.00840.0040.0713-0.0043-0.00490.0339-0.00180.002516.6224-15.1153-42.6242
40.12650.0353-0.1750.27590.00530.26240.00530.0195-0.00050.0179-0.01080.0017-0.0036-0.04190.00540.03460.003-0.00890.03750.01120.02496.2014-7.0549-22.7708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 89
2X-RAY DIFFRACTION2A90 - 192
3X-RAY DIFFRACTION3A193 - 250
4X-RAY DIFFRACTION4A251 - 410

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