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- PDB-2i6d: The structure of a putative RNA methyltransferase of the TrmH fam... -

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Basic information

Entry
Database: PDB / ID: 2i6d
TitleThe structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.
ComponentsRNA methyltransferase, TrmH family
KeywordsTRANSFERASE / RNA methyltransferase / TrmH family / stuctural genomics / Porphyromonas gingivalis / knot / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


RNA methyltransferase activity / RNA processing / RNA binding
Similarity search - Function
tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / Ribosomal protein L30/S12 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / 2-Layer Sandwich ...tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / Ribosomal protein L30/S12 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / RNA methyltransferase, TrmH family
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsCuff, M.E. / Mussar, K.E. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.
Authors: Cuff, M.E. / Mussar, K.E. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA methyltransferase, TrmH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4482
Polymers28,3881
Non-polymers601
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA methyltransferase, TrmH family
hetero molecules

A: RNA methyltransferase, TrmH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8954
Polymers56,7752
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2890 Å2
ΔGint-20 kcal/mol
Surface area22870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.921, 107.119, 120.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

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Components

#1: Protein RNA methyltransferase, TrmH family


Mass: 28387.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: SpoU, PG_0744 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): TIGR4
References: UniProt: Q7MW92, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.8M NaH2PO4, 1.2M K2HPO4, 0.1M Acetate pH 4.5, 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: 0.97951, 0.97962
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979511
20.979621
ReflectionResolution: 1.85→37.1 Å / Num. all: 23206 / Num. obs: 23206 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.35 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.85→37.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.447 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.145
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1193 5.1 %RANDOM
Rwork0.18892 ---
obs0.19126 22012 98.33 %-
all-23206 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.802 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 4 315 2252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222069
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9862829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46322.41487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60115347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0331522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021591
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21426
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9961.51344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36622124
X-RAY DIFFRACTIONr_scbond_it2.2943812
X-RAY DIFFRACTIONr_scangle_it3.3174.5699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 65 -
Rwork0.251 1386 -
obs--85 %
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)
13.7396-0.0142-0.03029.0521-0.52821.87030.1795-0.08090.11570.3451-0.1299-0.1034-0.3990.1765-0.04960.04730.0003-0.03-0.06-0.0503-0.0389.923522.979151.2669
24.2184-1.58450.14749.2552-1.48013.98870.1353-0.08630.1842-0.3142-0.03260.46660.0301-0.055-0.10270.02620.0115-0.0351-0.0927-0.06410.04832.162423.90347.4925
32.9642-0.33941.25085.81130.02663.7161-0.1304-0.29290.24430.2335-0.0314-0.0047-0.37560.12810.1618-0.09730.0141-0.0567-0.1091-0.0542-0.124523.40226.14945.0214
48.89394.39348.68342.54533.754716.4446-0.1105-0.13310.07480.0238-0.07210.141-0.0405-0.32170.1826-0.15830.0652-0.0077-0.149-0.0531-0.094916.29611.673842.7268
58.2918-3.83261.05933.0337-2.14573.3686-0.0027-0.10860.2160.030.0083-0.1426-0.56170.0301-0.00560.0250.0057-0.0076-0.072-0.1135-0.042918.931811.641646.3851
64.59630.73180.77642.51531.47894.590.033-0.2081-0.1272-0.06820.0816-0.06860.22640.7988-0.1147-0.12110.064-0.03690.04750.0077-0.141231.5661-2.747644.3431
72.3454-1.5161-0.03884.2406-1.17744.4387-0.02040.1354-0.04-0.35740.0304-0.17450.22280.5335-0.01-0.08210.0291-0.0441-0.0546-0.032-0.125527.4571-3.29933.0952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 443 - 47
2X-RAY DIFFRACTION2AA45 - 9348 - 96
3X-RAY DIFFRACTION3AA94 - 11897 - 121
4X-RAY DIFFRACTION4AA119 - 130122 - 133
5X-RAY DIFFRACTION5AA131 - 162134 - 165
6X-RAY DIFFRACTION6AA163 - 216166 - 219
7X-RAY DIFFRACTION7AA217 - 254220 - 257

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