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- PDB-4ig6: Crystal structure of a tRNA (guanine-N1)-methyltransferase from A... -

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Basic information

Entry
Database: PDB / ID: 4ig6
TitleCrystal structure of a tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum bound to S-adenosylhomocysteine
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tRNA modification / S-adenosyl methionine-dependent / SAM / SAH / S-adenosyl homocysteine / natural inhibitor / tRNA / M1G / G37 / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum bound to S-adenosylhomocysteine
Authors: Edwards, T.E. / Clifton, M.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5314
Polymers28,0761
Non-polymers4553
Water2,540141
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0638
Polymers56,1522
Non-polymers9116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8200 Å2
ΔGint-64 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.110, 105.110, 92.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 28075.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: APH_1267, trmD / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2GIL5, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 4.54 Å3/Da / Density % sol: 72.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: AnphA.00316.a.A1 PS00323 at 21 mg/mL with 3 mM SAH against JCSG+ A4: 30% MPD, 20 mM calcium chloride, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 24, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 20842 / Num. obs: 20785 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 40.675 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.5364.3111296150199.9
2.46-2.530.455.0611105147799.9
2.53-2.60.3865.8410752142099.7
2.6-2.680.3546.410502139099.9
2.68-2.770.2757.5510221135099.8
2.77-2.870.219.42100131318100
2.87-2.980.16911.2296201266100
2.98-3.10.15412.7492011212100
3.1-3.240.12415.458774116599.8
3.24-3.390.08519.268609113399.9
3.39-3.580.06925.381061067100
3.58-3.790.05433.397709101799.8
3.79-4.060.04737.297252964100
4.06-4.380.04143.3679591399.9
4.38-4.80.03452.57616182699.9
4.8-5.370.03846.12555475999.7
5.37-6.20.04339.42495468899.6
6.2-7.590.04338.32417357999.7
7.59-10.730.02262.76324646898.3
10.730.0268.67163027292.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å41.88 Å
Translation3 Å41.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KNU

3knu


Resolution: 2.4→41.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.169 / WRfactor Rwork: 0.1452 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8811 / SU B: 7.597 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1706 / SU Rfree: 0.1551 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 1064 5.1 %RANDOM
Rwork0.1752 ---
obs0.1767 20749 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.31 Å2 / Biso mean: 35.5847 Å2 / Biso min: 19.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0 Å2
2---0.71 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 28 141 1885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191807
X-RAY DIFFRACTIONr_bond_other_d0.0010.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9912458
X-RAY DIFFRACTIONr_angle_other_deg0.74433983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9425230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63323.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34515304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6711515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_mcbond_it1.9942.804902
X-RAY DIFFRACTIONr_mcbond_other1.9942.804901
X-RAY DIFFRACTIONr_mcangle_it3.3584.1911126
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 74 -
Rwork0.222 1419 -
all-1493 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -14.8063 Å / Origin y: 16.8591 Å / Origin z: -16.3539 Å
111213212223313233
T0.0279 Å20.0269 Å20.0261 Å2-0.0659 Å20.031 Å2--0.0452 Å2
L0.6652 °20.7874 °2-0.0428 °2-1.0721 °2-0.0229 °2--0.1376 °2
S0.0058 Å °-0.1044 Å °-0.0477 Å °0.0161 Å °-0.0557 Å °-0.0562 Å °0.0015 Å °0.0241 Å °0.0499 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 222
2X-RAY DIFFRACTION1A301

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