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- PDB-3ay0: Crystal structure of Methanocaldococcus jannaschii Trm5 in comple... -

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Basic information

Entry
Database: PDB / ID: 3ay0
TitleCrystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine
ComponentsUncharacterized protein MJ0883
KeywordsTRANSFERASE / Rossmann Fold / methyltransferase / AdoMet binding
Function / homology
Function and homology information


tRNA methyltransferase activity / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / tRNA methylation / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #2580 / tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / : / : / TYW2 N-terminal domain / SAM-dependent methyltransferase TRM5/TYW2-type / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / TRM5/TYW2 methyltransferase domain ...Alpha-Beta Plaits - #2580 / tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / : / : / TYW2 N-terminal domain / SAM-dependent methyltransferase TRM5/TYW2-type / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / TRM5/TYW2 methyltransferase domain / GMP Synthetase; Chain A, domain 3 / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / tRNA (guanine(37)-N(1))-methyltransferase Trm5b
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsGoto-Ito, S. / Ito, T. / Hou, Y.M. / Yokoyama, S.
CitationJournal: Rna / Year: 2011
Title: Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.
Authors: Lahoud, G. / Goto-Ito, S. / Yoshida, K. / Ito, T. / Yokoyama, S. / Hou, Y.M.
History
DepositionApr 21, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0883
B: Uncharacterized protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0059
Polymers78,1442
Non-polymers8627
Water23413
1
A: Uncharacterized protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5355
Polymers39,0721
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein MJ0883
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4704
Polymers39,0721
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.490, 67.127, 92.239
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein MJ0883 / tRNA (guanine-N(1)-)-methyltransferase


Mass: 39071.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0883, Trm5 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q58293
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.02M HEPES, 0.175M sodium thiocyanate, 8% PEG 3350, 5% PEGMME 550, 0.002M zinc sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 14439 / % possible obs: 99.8 % / Observed criterion σ(I): -2 / Redundancy: 3.7 % / Biso Wilson estimate: 86.7 Å2 / Rsym value: 0.109 / Net I/σ(I): 13.3
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 706 / Rsym value: 0.468 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YX1

2yx1


Resolution: 3.05→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.2932 724 RANDOM
Rwork0.2142 --
all-14491 -
obs-14426 -
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 43 13 5232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.48121
X-RAY DIFFRACTIONc_bond_d0.007797

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