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- PDB-5vm8: Crystal structure of a Ribosomal RNA small subunit methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 5vm8
TitleCrystal structure of a Ribosomal RNA small subunit methyltransferase E from Neisseria gonorrhoeae bound to S-adenosyl methionine
ComponentsRibosomal RNA small subunit methyltransferase E
KeywordsTRANSFERASE / NIAID / SAM / SAH / RNA methyltransferase / protein knot / trefoil knot / 2 domain protein / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


16S rRNA (uracil1498-N3)-methyltransferase / methyltransferase activity / rRNA processing / methylation / cytoplasm
Similarity search - Function
Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / : / Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a Ribosomal RNA small subunit methyltransferase E from Neisseria gonorrhoeae bound to S-adenosyl methionine
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Edwards, T.E. / Conrady, D.G. / Lorimer, D.D.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase E
B: Ribosomal RNA small subunit methyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0823
Polymers55,6842
Non-polymers3981
Water1,15364
1
A: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)27,8421
Polymers27,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal RNA small subunit methyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2402
Polymers27,8421
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-11 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.300, 71.540, 120.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 8 or (resid 9...
21(chain B and (resid 0 through 7 or (resid 8...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLUGLU(chain A and (resid 0 through 8 or (resid 9...AA0 - 88 - 16
12ASNASNASNASN(chain A and (resid 0 through 8 or (resid 9...AA917
13HISHISTHRTHR(chain A and (resid 0 through 8 or (resid 9...AA0 - 2418 - 249
14HISHISTHRTHR(chain A and (resid 0 through 8 or (resid 9...AA0 - 2418 - 249
15HISHISTHRTHR(chain A and (resid 0 through 8 or (resid 9...AA0 - 2418 - 249
16HISHISTHRTHR(chain A and (resid 0 through 8 or (resid 9...AA0 - 2418 - 249
21HISHISPROPRO(chain B and (resid 0 through 7 or (resid 8...BB0 - 78 - 15
22GLUGLUASNASN(chain B and (resid 0 through 7 or (resid 8...BB8 - 916 - 17
23HISHISSAMSAM(chain B and (resid 0 through 7 or (resid 8...BB - C0 - 3018
24HISHISSAMSAM(chain B and (resid 0 through 7 or (resid 8...BB - C0 - 3018
25HISHISSAMSAM(chain B and (resid 0 through 7 or (resid 8...BB - C0 - 3018
26HISHISSAMSAM(chain B and (resid 0 through 7 or (resid 8...BB - C0 - 3018

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase E


Mass: 27841.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: rsmE, WHOW_01089 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D3F5D3, UniProt: Q5F4Y3*PLUS, 16S rRNA (uracil1498-N3)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: NegoA.00176.a.B1.PW37905 at 20 mg/mL with 4 mM SAM against JCSG+ screen condition C4 10% PEG 6000, 0.1 M Hepes pH 7.0 supplemented with 20% EG and 2.5 mM AMP as cryo-protectant, crystal ...Details: NegoA.00176.a.B1.PW37905 at 20 mg/mL with 4 mM SAM against JCSG+ screen condition C4 10% PEG 6000, 0.1 M Hepes pH 7.0 supplemented with 20% EG and 2.5 mM AMP as cryo-protectant, crystal tracking ID 273658c4. unique puck ID llm2-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→28.944 Å / Num. obs: 21718 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.906 % / Biso Wilson estimate: 51.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.051 / Χ2: 1.035 / Net I/σ(I): 21.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.464.7440.5522.6916080.8570.61499.4
2.46-2.535.0070.3733.815500.9460.41399.4
2.53-2.64.9680.3614.314960.9470.499.3
2.6-2.685.0060.2865.4314580.9590.31799
2.68-2.775.0170.2157.0814390.9750.23799.2
2.77-2.874.9840.1689.0413870.9870.18699
2.87-2.985.0160.11912.2913210.9930.13299.1
2.98-3.14.9640.08416.6812830.9960.09398.8
3.1-3.244.9460.06620.8512330.9970.07399
3.24-3.394.9720.05523.9411820.9980.06198.8
3.39-3.584.8940.04628.4311370.9990.05198.4
3.58-3.794.9110.04133.0410580.9990.04598.7
3.79-4.064.8890.03240.669860.9990.03698.2
4.06-4.384.8850.02844.749530.9990.03298.1
4.38-4.84.8040.02746.338580.9990.0397.6
4.8-5.374.8210.02745.827770.9990.03197.4
5.37-6.24.7710.02645.416940.9990.02996.7
6.2-7.594.7580.02548.895920.9990.02895.3
7.59-10.734.6330.0253.054600.9990.02393.3
10.73-28.9443.890.01846.0824610.02183.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nxz

1nxz


Resolution: 2.4→28.944 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.28
RfactorNum. reflection% reflection
Rfree0.2536 1902 8.77 %
Rwork0.1954 --
obs0.2006 21682 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.22 Å2 / Biso mean: 66.3046 Å2 / Biso min: 21.79 Å2
Refinement stepCycle: final / Resolution: 2.4→28.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 27 64 3562
Biso mean--55.91 52.92 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083565
X-RAY DIFFRACTIONf_angle_d1.0154873
X-RAY DIFFRACTIONf_chiral_restr0.057582
X-RAY DIFFRACTIONf_plane_restr0.007642
X-RAY DIFFRACTIONf_dihedral_angle_d16.5222157
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1907X-RAY DIFFRACTION12.042TORSIONAL
12B1907X-RAY DIFFRACTION12.042TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-2.46020.33511420.2871402154499
2.4602-2.52660.34991240.25891407153199
2.5266-2.60090.35571430.25051395153899
2.6009-2.68480.34171320.24061385151799
2.6848-2.78070.30041530.24021392154599
2.7807-2.8920.30791250.23971427155299
2.892-3.02350.28831380.22821415155399
3.0235-3.18270.33731450.22351399154499
3.1827-3.38180.26831240.22861410153499
3.3818-3.64240.29411350.22181420155599
3.6424-4.00810.24081390.17791425156499
4.0081-4.58610.19451440.14831410155498
4.5861-5.77050.21311300.16811449157997
5.7705-28.9460.21131280.17281444157293
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)
15.1349-3.23991.23112.1992-0.58070.5963-0.1108-1.35340.45150.95430.6828-0.39470.12120.15620.12791.27850.0507-0.24530.9013-0.01580.390813.988816.61130.0754
25.1268-2.62723.02271.2414-1.32794.5982-0.3331-0.7418-0.48721.68440.2792-0.1512-0.01880.23020.0441.2090.1393-0.32770.72310.02660.660916.560315.3847-3.1591
37.02140.52830.46663.58810.32391.5238-0.0948-0.3102-0.23730.60930.01550.09140.2887-0.04680.08530.41750.00260.01770.2728-0.0020.2415-0.716.9361-19.3029
46.99976.20923.38699.0660.38163.58910.1239-0.68970.92351.2993-0.76311.2692-0.3028-0.62890.83310.5180.06090.09230.643-0.14540.6498-8.706132.0225-22.9132
57.4621-2.8173-1.37817.678-0.87333.53340.17790.6470.2705-0.45490.05230.62-0.359-0.4408-0.10120.38870.07250.04820.3938-0.01390.3834-5.961531.3376-31.4358
67.2322-2.9994-1.67076.6637-1.11352.92290.02940.04480.53280.0627-0.1166-0.4639-0.22020.08090.12310.2827-0.0178-0.03240.25170.06670.36564.938229.3508-30.539
77.27822.55193.95264.41851.1763.21390.20540.9657-0.5665-1.2656-0.0794-0.34230.325-0.02-0.10560.92210.1515-0.0290.7229-0.07050.40222.646710.4559-56.8241
83.55961.63853.25871.68123.05355.51390.09110.06030.3521-1.88740.1576-0.1894-0.9035-1.1890.06021.35210.2121-0.18090.83250.28120.72436.761722.6749-54.544
93.0007-0.86090.9243.52361.33274.63680.32710.1140.1223-0.2769-0.0494-0.9670.27930.4269-0.21040.3813-0.00730.09890.3621-0.02820.654420.917714.3563-38.1888
105.85670.1042-0.17321.67441.61292.5145-0.0935-0.14230.60580.14250.1528-1.621-0.39660.68150.00250.3975-0.0709-0.01770.4874-0.07040.989923.470926.6704-29.6155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )A0 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 76 )A20 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 152 )A77 - 152
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 169 )A153 - 169
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 207 )A170 - 207
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 241 )A208 - 241
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 59 )B0 - 59
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 76 )B60 - 76
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 164 )B77 - 164
10X-RAY DIFFRACTION10chain 'B' and (resid 165 through 241 )B165 - 241

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