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- PDB-5a7y: Crystal structure of Sulfolobus acidocaldarius Trm10 in complex w... -

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Basic information

Entry
Database: PDB / ID: 5a7y
TitleCrystal structure of Sulfolobus acidocaldarius Trm10 in complex with S-adenosylhomocysteine
ComponentsTRNA (ADENINE(9)-N1)-METHYLTRANSFERASE
KeywordsTRANSFERASE / SPOUT / TRNA METHYLTRANSFERASE / TRM10
Function / homology
Function and homology information


tRNA (adenine9-N1)-methyltransferase / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA methylation / tRNA processing / cytoplasm
Similarity search - Function
: / tRNA methyltransferase, archaea / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile.
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (adenine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVan Laer, B. / Roovers, M. / Wauters, L. / Kasprzak, J. / Dyzma, M. / Deyaert, E. / Feller, A. / Bujnicki, J. / Droogmans, L. / Versees, W.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural and Functional Insights Into tRNA Binding and Adenosine N1-Methylation by an Archaeal Trm10 Homologue.
Authors: Van Laer, B. / Roovers, M. / Wauters, L. / Kasprzak, J.M. / Dyzma, M. / Deyaert, E. / Kumar Singh, R. / Feller, A. / Bujnicki, J.M. / Droogmans, L. / Versees, W.
History
DepositionJul 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 (ADENINE(9)-N1)-METHYLTRANSFERASE
B: TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8458
Polymers70,7462
Non-polymers1,0996
Water34219
1
A: TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8633
Polymers35,3731
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9825
Polymers35,3731
Non-polymers6094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.140, 101.090, 66.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 0 - 290 / Label seq-ID: 20 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.94774, 0.319043, -0.000365), (0.318986, 0.94755, -0.019939), (-0.006016, -0.019014, -0.999801)80.6337, -11.7824, 99.09688

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Components

#1: Protein TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE / TRNA(M1A9)-METHYLTRANSFERASE / TRNA(M1A9)MTASE / TRM10


Mass: 35372.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic)
Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q4J894, tRNA (adenine9-N1)-methyltransferase
#2: Chemical ChemComp-SAH / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 4.5
Details: 0.4 M (NH4)2SO4, 0.1 M SODIUM ACETATE PH 4.5, 15-20 % PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98536
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98536 Å / Relative weight: 1
ReflectionResolution: 2.5→48.1 Å / Num. obs: 22754 / % possible obs: 99.1 % / Observed criterion σ(I): 1.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 13.26
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 1.56 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A7T

5a7t


Resolution: 2.5→48.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.652 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28923 1138 5 %RANDOM
Rwork0.23439 ---
obs0.23713 21616 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---5.08 Å20 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 74 19 4466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194506
X-RAY DIFFRACTIONr_bond_other_d00.024556
X-RAY DIFFRACTIONr_angle_refined_deg1.4922.0086058
X-RAY DIFFRACTIONr_angle_other_deg3.449310486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024894
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02950
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3892.4042196
X-RAY DIFFRACTIONr_mcbond_other2.382.3992193
X-RAY DIFFRACTIONr_mcangle_it3.6563.5842732
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.482.8712310
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 84 -
Rwork0.347 1604 -
obs--99.24 %
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)
15.343-3.2270.494812.0875-1.20911.2707-0.058-0.00230.88140.17710.1514-0.5063-0.14380.1678-0.09340.1402-0.0114-0.06790.8012-0.01250.220731.50350.20729.023
219.0485-23.4801-18.222143.194921.904140.59620.0235-0.20250.4815-0.98170.17250.2961-0.3862-0.2799-0.1960.0928-0.0886-0.13220.6180.16580.40923.27644.41826.61
34.6179-0.3909-0.1371.27160.52114.5407-0.0270.1512-0.1812-0.05340.0030.12510.1955-0.08550.02410.1010.0059-0.02040.89520.01710.020236.78220.73131.853
45.7138-10.77469.565121.0802-23.272954.3759-1.0673-0.2378-0.17182.02090.22920.16-3.4332.56650.83821.8119-0.4106-0.39831.62560.07611.454637.6279.6731.318
56.5623-0.40683.27311.2733-0.22575.30160.01710.0690.1016-0.16340.1339-0.2406-0.06390.6859-0.1510.0254-0.02230.03731.0752-0.02190.060355.86624.01737.494
610.8234-4.771410.41322.504-14.300719.2648-0.2108-0.11941.09051.0774-0.2973-1.3113-1.0060.74530.50820.2395-0.03420.10691.1284-0.21570.404163.75526.70552.677
76.35160.7021-1.37545.9608-0.15923.75240.56370.0940.95640.1777-0.3056-0.2431-0.68010.1037-0.25820.14440.00830.08090.8044-0.01280.181966.80942.86469.299
85.16751.20282.73974.07271.1248.04320.08690.4065-0.4676-0.01750.0105-0.14410.73040.4481-0.09740.07570.04190.01170.9083-0.08460.061154.45117.53761.271
95.0474-0.1333-0.0470.75940.65493.53970.2486-0.4029-0.40310.01260.0184-0.00990.36920.1062-0.26710.07410.0864-0.04260.92840.05580.057849.43117.09870.55
1017.4474-2.446217.555515.98718.875726.02620.78070.74580.5079-0.116-1.2113-0.06971.1386-0.02080.43071.0072-0.03310.11511.2720.00521.129844.2265.67266.249
115.7135-0.66162.250.2187-1.07165.5164-0.07280.0080.21980.02590.0494-0.014-0.13-0.31440.02350.00520.0497-0.00380.9413-0.05180.013737.59825.6862.049
125.1588-1.17242.85357.0114.563310.6877-0.1357-0.12620.70950.02220.1585-0.2125-1.1264-0.6775-0.02270.22720.07280.05330.87950.0670.1327.94134.00850.305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 73
2X-RAY DIFFRACTION2A74 - 83
3X-RAY DIFFRACTION3A84 - 181
4X-RAY DIFFRACTION4A182 - 202
5X-RAY DIFFRACTION5A203 - 275
6X-RAY DIFFRACTION6A276 - 291
7X-RAY DIFFRACTION7B0 - 86
8X-RAY DIFFRACTION8B87 - 132
9X-RAY DIFFRACTION9B133 - 184
10X-RAY DIFFRACTION10B191 - 201
11X-RAY DIFFRACTION11B202 - 265
12X-RAY DIFFRACTION12B266 - 290

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