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- PDB-4fmw: Crystal structure of methyltransferase domain of human RNA (guani... -

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Basic information

Entry
Database: PDB / ID: 4fmw
TitleCrystal structure of methyltransferase domain of human RNA (guanine-9-) methyltransferase domain containing protein 2
ComponentsRNA (guanine-9-)-methyltransferase domain-containing protein 2
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / RNA modification / RNA methylation / RNA methyltransferase / guanine
Function / homology
Function and homology information


mitochondrial tRNA processing / : / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA N1-guanine methylation / tRNA modification in the nucleus and cytosol / tRNA methylation / actin cytoskeleton / tRNA binding / nucleolus ...mitochondrial tRNA processing / : / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA N1-guanine methylation / tRNA modification in the nucleus and cytosol / tRNA methylation / actin cytoskeleton / tRNA binding / nucleolus / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Alpha/beta knot - #30 / tRNA (guanine(9)-N(1))-methyltransferase TRM10/TRM10A / tRNA (guanine-N1-)-methyltransferase, eukaryotic / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / Alpha/beta knot / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / tRNA methyltransferase 10 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDong, A. / Zeng, H. / Loppnau, P. / Tempel, W. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of methyltransferase domain of human RNA (guanine-9-) methyltransferase domain containing protein 2
Authors: Zeng, H. / Dong, A. / Loppnau, P. / Tempel, W. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Wu, H.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (guanine-9-)-methyltransferase domain-containing protein 2
B: RNA (guanine-9-)-methyltransferase domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,48828
Polymers46,4942
Non-polymers99426
Water2,468137
1
A: RNA (guanine-9-)-methyltransferase domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,69413
Polymers23,2471
Non-polymers44612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (guanine-9-)-methyltransferase domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,79515
Polymers23,2471
Non-polymers54814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.097, 43.309, 60.347
Angle α, β, γ (deg.)100.43, 90.03, 92.88
Int Tables number1
Space group name H-MP1
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RNA (guanine-9-)-methyltransferase domain-containing protein 2


Mass: 23247.141 Da / Num. of mol.: 2 / Fragment: UNP residues 82-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RG9MTD2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)V2RpRARE
References: UniProt: Q8TBZ6, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 20 / Source method: obtained synthetically
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.22 M NH4SO4, 0.1 M Tris-HCl, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97903 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24649 / Num. obs: 24649 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 25.87 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 5 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.42 / Num. unique all: 1199 / Rsym value: 0.571 / % possible all: 96.4

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Processing

Software
NameVersionClassification
CLSMXDCdata collection
SOLVEphasing
RESOLVEmodel building
BUSTER2.10.0refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.99 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.9036 / SU R Cruickshank DPI: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 804 3.26 %RANDOM
Rwork0.2184 ---
all0.2193 24649 --
obs0.2193 24649 95.9 %-
Displacement parametersBiso mean: 29.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.469 Å22.0768 Å2-0.0627 Å2
2---2.1412 Å2-0.0833 Å2
3----0.3278 Å2
Refine analyzeLuzzati coordinate error obs: 0.283 Å
Refinement stepCycle: LAST / Resolution: 2→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 85 137 3025
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092967HARMONIC1.5
X-RAY DIFFRACTIONt_angle_deg0.924032HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1032SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes454HARMONIC5
X-RAY DIFFRACTIONt_it2967HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion18.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion390SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3468SEMIHARMONIC4
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2504 85 3.33 %
Rwork0.226 2470 -
all0.2268 2555 -
obs--95.9 %
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)
11.2848-0.35340.25031.2831-0.56650.84510.00710.03730.04420.024-0.00430.0290.0457-0.0084-0.0028-0.0697-0.0328-0.00090.0460.0293-0.08510.638218.871146.02
21.2174-0.1719-0.12690.72290.46971.20730.0129-0.0062-0.06440.03520.0141-0.0196-0.07490.0208-0.027-0.0754-0.0235-0.01670.06520.0364-0.086823.459112.2114.0893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|94 - A|275 A|301 - A|301 }A94 - 275
2X-RAY DIFFRACTION1{ A|94 - A|275 A|301 - A|301 }A301
3X-RAY DIFFRACTION2{ B|95 - B|274 B|301 - B|301 }B95 - 274
4X-RAY DIFFRACTION2{ B|95 - B|274 B|301 - B|301 }B301

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