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- PDB-2qm3: Crystal structure of a predicted methyltransferase from Pyrococcu... -

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Basic information

Entry
Database: PDB / ID: 2qm3
TitleCrystal structure of a predicted methyltransferase from Pyrococcus furiosus
ComponentsPredicted methyltransferase
KeywordsTRANSFERASE / putative methyltransferase / structural genomics / Pyrococcus furiosus / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N4-bis(aminopropyl)spermidine synthase / polyamine biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / cytoplasm
Similarity search - Function
N(4)-bis(aminopropyl)spermidine synthase, C-terminal / N(4)-bis(aminopropyl)spermidine synthase / Branched-chain polyamine synthase A C-terminal domain / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle ...N(4)-bis(aminopropyl)spermidine synthase, C-terminal / N(4)-bis(aminopropyl)spermidine synthase / Branched-chain polyamine synthase A C-terminal domain / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / N(4)-bis(aminopropyl)spermidine synthase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsCuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a predicted methyltransferase from Pyrococcus furiosus.
Authors: Cuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6126
Polymers43,3521
Non-polymers2605
Water4,017223
1
A: Predicted methyltransferase
hetero molecules

A: Predicted methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,22512
Polymers86,7042
Non-polymers52110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.382, 85.262, 53.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsAuthors state that the biological unit of this protein is experimentally unknown, and that the dimeric assembly shown in remark 350 is a prediction based on crystal packing.

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Components

#1: Protein Predicted methyltransferase / Uncharacterized protein PF1111


Mass: 43352.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Species: Pyrococcus furiosus / Strain: DSM 3638, JCM 8422, Vc1 / Gene: PF1111 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U1U4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M Calcium acetate, 10% PEG 8000, 4% Butyrolactone, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97932
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979321
ReflectionResolution: 2.05→39.9 Å / Num. all: 22125 / Num. obs: 22125 / % possible obs: 95.09 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.415 / % possible all: 73.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.05→39.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.626 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.178
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. The link (residues 88 through 99) between the N- and C-terminal structural domains is missing. For the two molecules related by the crystallographic 2-fold axis, the pairing of domains is ...Details: 1. The link (residues 88 through 99) between the N- and C-terminal structural domains is missing. For the two molecules related by the crystallographic 2-fold axis, the pairing of domains is ambiguous. The authors have modeled the more compact combination, but the other remains possible given the data at hand. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22657 1189 5.1 %RANDOM
Rwork0.18296 ---
obs0.18518 22125 95.09 %-
all-22125 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---1.84 Å20 Å2
3---3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 14 223 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9783910
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84524.138145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83515521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9521522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022196
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21324
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.51758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40522790
X-RAY DIFFRACTIONr_scbond_it2.28231268
X-RAY DIFFRACTIONr_scangle_it3.5174.51115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 65 -
Rwork0.233 1258 -
obs--74.16 %
Refinement TLS params.Method: refined / Origin x: 47.9988 Å / Origin y: 12.366 Å / Origin z: 42.8343 Å
111213212223313233
T-0.0734 Å2-0.0193 Å20.0102 Å2--0.0967 Å2-0.098 Å2---0.1143 Å2
L3.3019 °2-0.4801 °20.0095 °2-1.3798 °2-0.0348 °2--0.2605 °2
S0.0489 Å °-0.4184 Å °0.5407 Å °0.0955 Å °-0.0205 Å °-0.1954 Å °-0.0725 Å °0.0086 Å °-0.0283 Å °

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