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- PDB-1uwv: Crystal Structure of RumA, the iron-sulfur cluster containing E. ... -

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Basic information

Entry
Database: PDB / ID: 1uwv
TitleCrystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase
Components23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
KeywordsTRANSFERASE / METHYLTRANSFERASE / RNA MODIFICATION / IRON-SULFUR CLUSTER / RNA PROCESSING
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 family signature 1. / RNA methyltransferase TrmA, conserved site / 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 family signature 1. / RNA methyltransferase TrmA, conserved site / 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
NICKEL (II) ION / PHOSPHATE ION / IRON/SULFUR CLUSTER / 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsLee, T.T. / Agarwalla, S. / Stroud, R.M.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Characterization of the 23 S Ribosomal RNA M5U1939 Methyltransferase from Escherichia Coli
Authors: Agarwalla, S. / Kealey, J.T. / Santi, D.V. / Stroud, R.M.
History
DepositionFeb 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2766
Polymers48,6771
Non-polymers5995
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.938, 99.448, 58.519
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48676.871 Da / Num. of mol.: 1
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 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P55135, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION 1939 (M-5-U1939) IN 23S RRNA. BELONGS TO ...CATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION 1939 (M-5-U1939) IN 23S RRNA. BELONGS TO THE RNA M5U METHYLTRANSFERASE FAMILY. RUMA
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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growpH: 9
Details: PROTEIN WAS CRYSTALLIZED FROM 50 MM TRIS-CL (PH 9-9.5), 10 MM NICL2, 12.5% GLYCEROL, AND 20% POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9.5 / PH range high: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
250 mMTris-Cl1reservoirpH9.0-9.5
310 mM1reservoirNiCl2
412.5 %glycerol1reservoir
520 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9786,0.9788
DetectorType: ADSC CCD QUANTUM-4 2X2 ARRAY / Detector: CCD / Date: Feb 15, 2002 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97881
ReflectionResolution: 1.95→50 Å / Num. obs: 29176 / % possible obs: 100 % / Observed criterion σ(I): 2.6 / Redundancy: 7.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.6 / % possible all: 100
Reflection
*PLUS
Num. measured all: 632764

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Processing

Software
NameVersionClassification
Quantamodel building
SCALEPACKdata scaling
CNSphasing
CCP4phasing
SHARPARP/WARPphasing
Quantaphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.386 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B-FACTORS ARE RESIDUAL B-FACTORS, (WHICH DO NOT INCLUDE THE CONTRIBUTION FROM THE TLS PARAMETERS). USE TLSANL (DISTRIBUTED WITH CCP4) TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B-FACTORS ARE RESIDUAL B-FACTORS, (WHICH DO NOT INCLUDE THE CONTRIBUTION FROM THE TLS PARAMETERS). USE TLSANL (DISTRIBUTED WITH CCP4) TO OBTAIN THE FULL B-FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1477 5.1 %RANDOM
Rwork0.186 ---
obs-27660 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.51 Å2
2---1.6 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 16 123 3378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213324
X-RAY DIFFRACTIONr_bond_other_d0.0020.023060
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.974501
X-RAY DIFFRACTIONr_angle_other_deg0.89237111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895416
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_restr0.10.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023683
X-RAY DIFFRACTIONr_gen_planes_other0.010.02645
X-RAY DIFFRACTIONr_nbd_refined0.2130.2600
X-RAY DIFFRACTIONr_nbd_other0.2470.23512
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.52079
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73723345
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.50631245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1554.51144
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 108
Rwork0.235 1941
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)
17.929511.913.467229.82133.61683.7214-0.2419-0.87220.57850.781-0.43391.56720.0492-0.62510.67580.39370.2112-0.03440.3429-0.1020.24814.4318-19.01119.9989
25.9474-5.44120.35396.96460.88026.6067-0.2087-0.2485-0.14990.95390.5126-0.3870.19160.0379-0.30390.29290.1614-0.1260.1347-0.03260.083815.9695-1.318518.9468
32.7327-0.8533-0.86322.12360.48990.7425-0.0384-0.01310.13750.12610.20450.23340.0935-0.1446-0.1660.13460.0117-0.00550.1653-0.0080.1462.277715.77739.9425
42.1226-3.0503-1.88755.22141.62695.5346-0.1256-0.0609-0.06110.09610.1666-0.52570.51680.2097-0.04090.08780.0641-0.07470.1444-0.05040.197424.1141-8.0023.5975
50.7662-0.97170.19484.4576-1.34032.5756-0.10710.0516-0.1198-0.08350.16210.24510.0591-0.2324-0.0550.0567-0.03230.0230.2172-0.03090.1515.35970.3561-14.5499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 74
2X-RAY DIFFRACTION2A75 - 93
3X-RAY DIFFRACTION2F1
4X-RAY DIFFRACTION3A125 - 262
5X-RAY DIFFRACTION4A94 - 124
6X-RAY DIFFRACTION5A263 - 431
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.66

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