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- PDB-3ffy: Putative tetrapyrrole (corrin/porphyrin) methyltransferase from B... -

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Basic information

Entry
Database: PDB / ID: 3ffy
TitlePutative tetrapyrrole (corrin/porphyrin) methyltransferase from Bacteroides fragilis.
ComponentsPutative tetrapyrrole (Corrin/porphyrin) methylase
Keywordsstructural genomics / unknown function / APC62130.1 / methyltransferase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


16S rRNA (cytidine1402-2'-O)-methyltransferase / : / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm
Similarity search - Function
SAM-dependent methyltransferase RsmI, conserved site / RsmI AdoMet-dependent methyltransferase protein family signature. / rRNA small subunit methyltransferase I / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily ...SAM-dependent methyltransferase RsmI, conserved site / RsmI AdoMet-dependent methyltransferase protein family signature. / rRNA small subunit methyltransferase I / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase I
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsOsipiuk, J. / Volkart, L. / Cobb, G. / Kim, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative tetrapyrrole (corrin/porphyrin) methyltransferase from Bacteroides fragilis.
Authors: Osipiuk, J. / Volkart, L. / Cobb, G. / Kim, Y. / Joachimiak, A.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative tetrapyrrole (Corrin/porphyrin) methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2553
Polymers13,0631
Non-polymers1922
Water66737
1
A: Putative tetrapyrrole (Corrin/porphyrin) methylase
hetero molecules

A: Putative tetrapyrrole (Corrin/porphyrin) methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5096
Polymers26,1252
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2230 Å2
ΔGint-67 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.536, 60.536, 96.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-5-

HOH

Detailsputative biological unit is a dimer based on PISA

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Components

#1: Protein Putative tetrapyrrole (Corrin/porphyrin) methylase


Mass: 13062.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF0585 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LHP3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.26 M ammonium sulfate, 0.1 M acetate buffer, 0.2 M sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→39.1 Å / Num. all: 11909 / Num. obs: 11909 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.636 / Net I/σ(I): 40.087
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.08 / Num. unique all: 355 / Χ2: 1.085 / % possible all: 57.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.288 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.796 / SU B: 10.945 / SU ML: 0.131 / SU R Cruickshank DPI: 0.228 / SU Rfree: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.156 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 572 4.8 %RANDOM
Rwork0.206 ---
all0.207 11852 --
obs0.207 11852 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.54 Å2 / Biso mean: 34.38 Å2 / Biso min: 20.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 2→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 10 37 937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022963
X-RAY DIFFRACTIONr_bond_other_d0.0010.02685
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.981309
X-RAY DIFFRACTIONr_angle_other_deg0.96231666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19522.60946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72515176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5041510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_mcbond_it0.9161.5576
X-RAY DIFFRACTIONr_mcbond_other0.1981.5230
X-RAY DIFFRACTIONr_mcangle_it1.7282943
X-RAY DIFFRACTIONr_scbond_it2.5413387
X-RAY DIFFRACTIONr_scangle_it4.1814.5360
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 21 -
Rwork0.319 493 -
all-514 -
obs-514 56.98 %
Refinement TLS params.Method: refined / Origin x: 3.8587 Å / Origin y: 23.9104 Å / Origin z: -1.5691 Å
111213212223313233
T0.2231 Å20.0056 Å20.0128 Å2-0.1946 Å2-0.009 Å2--0.0404 Å2
L3.5364 °2-0.7814 °21.12 °2-3.3881 °20.7637 °2--3.5371 °2
S0.0052 Å °-0.2364 Å °0.2037 Å °0.0902 Å °0.1093 Å °0.1017 Å °-0.3401 Å °-0.251 Å °-0.1145 Å °

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