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- PDB-2bh2: Crystal Structure of E. coli 5-methyluridine methyltransferase Ru... -

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Basic information

Entry
Database: PDB / ID: 2bh2
TitleCrystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.
Components
  • 23S RIBOSOMAL RNA 1932-1968
  • 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
KeywordsTRANSFERASE / IRON-SULFUR CLUSTER / METHYLTRANSFERASE / RNA MODIFICATION / RNA PROCESSING / RUMA / BASE FLIPPING / SAM / OB-FOLD / PROTEIN-RNA COMPLEX / BASE STACKING / SUBSTRATE SELECTIVITY / GENERAL BASE / PRODUCT RELEASE / 4FE-4S / METAL-BINDING
Function / homology
Function and homology information


23S rRNA (uracil1939-C5)-methyltransferase / rRNA (uridine-C5-)-methyltransferase activity / rRNA base methylation / 4 iron, 4 sulfur cluster binding / iron ion binding / RNA binding
Similarity search - Function
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1070 / RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain ...23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1070 / RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. / Nucleic acid-binding proteins / Vaccinia Virus protein VP39 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLee, T.T. / Agarwalla, S. / Stroud, R.M.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2005
Title: A Unique RNA Fold in the Ruma-RNA-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function
Authors: Lee, T.T. / Agarwalla, S. / Stroud, R.M.
#1: Journal: Structure / Year: 2004
Title: Crystal Structure of Ruma, an Iron-Sulfur Cluster Containing E. Coli Ribosomal RNA 5-Methyluridine Methyltransferase
Authors: Lee, T.T. / Agarwalla, S. / Stroud, R.M.
History
DepositionJan 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
B: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
C: 23S RIBOSOMAL RNA 1932-1968
D: 23S RIBOSOMAL RNA 1932-1968
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4658
Polymers119,9924
Non-polymers1,4724
Water6,125340
1
A: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
C: 23S RIBOSOMAL RNA 1932-1968
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7324
Polymers59,9962
Non-polymers7362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
D: 23S RIBOSOMAL RNA 1932-1968
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7324
Polymers59,9962
Non-polymers7362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)190.061, 63.542, 112.019
Angle α, β, γ (deg.)90.00, 125.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA / 23S RRNA(M-5-U1939)-METHYLTRANSFERASE / 23S RRNA URACIL-5-METHYLTRANSFERASE RUMA


Mass: 48114.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: IRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND CYS162
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P55135, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain 23S RIBOSOMAL RNA 1932-1968


Mass: 11882.091 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 5-FLUORO-U1939 IS METHYLATED AND ITS 6-C IS COVALENTLY LINKED TO CYS389 OF RUMA
Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: 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
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Compound detailsS-ADENOSYL-L-METHIONINE => S-ADENOSYL-L-HOMOCYSTEINE + RRNA + RRNA CONTAINING THYMINE. CATALYZES ...S-ADENOSYL-L-METHIONINE => S-ADENOSYL-L-HOMOCYSTEINE + RRNA + RRNA CONTAINING THYMINE. CATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION 1939 (M-5-U1939) IN 23S RRNA. BELONGS TO THE RNA M5U METHYLTRANSFERASE FAMILY.

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5
Details: RUMA-RNA-SAH COMPLEX WAS CRYSTALLIZED FROM 100 MM SODIUM CACODYLATE, PH 6.5, 1.5 M AMMONIUM SULFATE, AND 10 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2003
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 59411 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWV

1uwv


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.547 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3002 5.1 %RANDOM
Rwork0.174 ---
obs0.177 56408 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å2-0.26 Å2
2--1.43 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 1274 68 340 8156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0218108
X-RAY DIFFRACTIONr_bond_other_d0.0020.026649
X-RAY DIFFRACTIONr_angle_refined_deg2.0112.17811280
X-RAY DIFFRACTIONr_angle_other_deg0.978315585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375832
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_restr0.110.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027996
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021290
X-RAY DIFFRACTIONr_nbd_refined0.2160.21398
X-RAY DIFFRACTIONr_nbd_other0.2490.27962
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.24604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2342
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.54168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53426707
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.86433940
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.284.54549
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 199
Rwork0.248 3990
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)
13.7948-4.12234.143514.9885-10.087314.8569-0.7991-1.1220.21831.65480.97490.0161-1.164-1.3807-0.17580.27860.1058-0.02350.535-0.07670.153699.50729.988136.7798
23.32330.45730.74031.73190.59661.93010.0569-0.46280.40620.0785-0.11420.288-0.2337-0.270.05730.10170.00120.01090.0678-0.03120.15167.678514.40822.906
33.00810.79410.5081.25420.71821.40790.09260.0115-0.39510.0542-0.0153-0.160.15680.2332-0.07720.0470.0055-0.0010.02250.02070.089781.8381-7.99112.115
41.21961.1955-0.18673.1654-1.926624.4443-0.3374-0.0745-0.84490.1294-0.4297-0.36461.9261.02590.76720.31850.00030.10580.25740.1040.41718.1465-35.233227.0436
52.78720.78730.16582.47020.23731.75280.00140.2908-0.1767-0.17030.0508-0.41380.07720.184-0.05210.0496-0.01190.01410.0122-0.02410.050144.6634-21.32827.7016
62.44931.1834-0.29851.9583-0.06540.96740.161-0.39930.40690.2143-0.16870.2583-0.1484-0.12360.00770.0514-0.00380.03770.0775-0.06820.093131.765-2.739424.9969
71.6396-1.01482.51010.4932-1.09772.1081-0.0481-0.5369-0.21170.15360.2320.12630.1264-0.2785-0.1840.3807-0.03720.02250.44310.04480.038383.0028-3.5535.5746
80.66960.0492-0.45170.74630.73242.0258-0.1027-0.7633-0.02040.39290.0531-0.05840.49950.10880.04960.3658-0.0069-0.02940.37690.0440.022335.5851-24.337333.5657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 74
2X-RAY DIFFRACTION2A75 - 93
3X-RAY DIFFRACTION2A1
4X-RAY DIFFRACTION2A125 - 262
5X-RAY DIFFRACTION3A94 - 124
6X-RAY DIFFRACTION3A263 - 432
7X-RAY DIFFRACTION3A500
8X-RAY DIFFRACTION4B16 - 74
9X-RAY DIFFRACTION5B75 - 93
10X-RAY DIFFRACTION5B1
11X-RAY DIFFRACTION5B125 - 262
12X-RAY DIFFRACTION6B94 - 124
13X-RAY DIFFRACTION6B263 - 431
14X-RAY DIFFRACTION6B500
15X-RAY DIFFRACTION7C1932 - 1961
16X-RAY DIFFRACTION8D1932 - 1961

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