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- PDB-4dzr: The crystal structure of protein-(glutamine-N5) methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 4dzr
TitleThe crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
ComponentsProtein-(Glutamine-N5) methyltransferase, release factor-specific
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / nucleic acid binding / metal ion binding
Similarity search - Function
Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / PrmC N-terminal domain / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / PrmC N-terminal domain / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.551 Å
AuthorsTan, K. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Authors: Tan, K. / Chhor, G. / Bearden, J. / Joachimiak, A.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-(Glutamine-N5) methyltransferase, release factor-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9874
Polymers23,7961
Non-polymers1913
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein-(Glutamine-N5) methyltransferase, release factor-specific
hetero molecules

A: Protein-(Glutamine-N5) methyltransferase, release factor-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9748
Polymers47,5912
Non-polymers3826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2800 Å2
ΔGint-37 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.766, 61.766, 122.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

ACT

21A-402-

ACT

DetailsExperimentally unknown. It is predicted the molecule is a monomer.

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Components

#1: Protein Protein-(Glutamine-N5) methyltransferase, release factor-specific


Mass: 23795.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 (bacteria)
Strain: subsp. acidocaldarius DSM 446 / Gene: Aaci_2779 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C8WUG7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE EXPRESSED PROTEIN WAS A FULL LENGTH PROTEIN WITH SEQUENCE: SNA(MSE) ...THE AUTHORS STATE THAT THE EXPRESSED PROTEIN WAS A FULL LENGTH PROTEIN WITH SEQUENCE: SNA(MSE)SEAKYFVARLLKAIAEQLPQSPAYRALPLDE RKRLAEREAEQIVAHALGWDRVKLLQSLGDEVPDEIAERAARLAALRVQGEPLAYVLGKQDF YGRTFEVGPDCLIPRPDTEVLVEEAIRFLKR(MSE)PSGTRVIDVGTGSGCIAVSIALACPG VSVTAVDLS(MSE)DALAVARRNAERFGAVVDWAAADGIEWLIERAERGRPWHAIVSNPPYI PTGEIDQLEPSVRDYEPRLALDGGEDGLQFYRR(MSE)AALPPYVLARGRAGVFLEVGHNQA DEVARLFAPWRERGFRVRKVKDLRGIDRVIAVTREPGSPPESENL AND SINCE TRYPSIN WAS ADDED IN PROTEIN FOR CRYSTALLIZATION PURPOSES, THE PROTEIN WAS CHOPPED AT MULTIPLE SITES. ESPECIALLY, AN EXPECTED N-TERMINAL DOMAIN WAS COMPLETELY GONE AND SEVERAL LOOPS ARE MISSING IN THE STRUCTURE. HOWEVER, THE AUTHORS DO NOT KNOW EXACTLY WHERE THE SEQUENCE STARTS.

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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: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium acetate hydrate, pH 7.5, 20% (w/v) PEG 3350, 0.0125mg/ml Trypsin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.97948
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979481
ReflectionResolution: 2.55→31 Å / Num. all: 8235 / Num. obs: 8235 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.8
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.2 / Num. unique all: 403 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.551→30.883 Å / SU ML: 0.82 / σ(F): 1.35 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 379 4.63 %random
Rwork0.2071 ---
obs0.2097 8179 99.38 %-
all-8179 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.155 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4262 Å20 Å2-0 Å2
2--4.4262 Å20 Å2
3----8.8525 Å2
Refinement stepCycle: LAST / Resolution: 2.551→30.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1255 0 11 5 1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091293
X-RAY DIFFRACTIONf_angle_d1.2041755
X-RAY DIFFRACTIONf_dihedral_angle_d14.615473
X-RAY DIFFRACTIONf_chiral_restr0.069195
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5512-2.92020.3471300.28552526X-RAY DIFFRACTION100
2.9202-3.67810.29721290.21162559X-RAY DIFFRACTION100
3.6781-30.88520.23771200.19252715X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.241 Å / Origin y: 14.54 Å / Origin z: 15.4956 Å
111213212223313233
T0.5504 Å20.1326 Å2-0.0581 Å2-0.4244 Å20.0217 Å2--0.2727 Å2
L2.8335 °20.7852 °2-0.3953 °2-5.3863 °21.0661 °2--10.6789 °2
S0.0771 Å °-0.398 Å °0.1045 Å °0.7514 Å °0.0235 Å °-0.0055 Å °0.1368 Å °-1.0472 Å °-0.0771 Å °
Refinement TLS groupSelection details: chain A

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