[English] 日本語
Yorodumi
- PDB-3p2k: Structure of an antibiotic related Methyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p2k
TitleStructure of an antibiotic related Methyltransferase
Components16S rRNA methylase
KeywordsTRANSFERASE / Methyltransferase / NpmA
Function / homology
Function and homology information


16S rRNA (adenine1408-N1)-methyltransferase / methyltransferase activity / methylation / response to antibiotic
Similarity search - Function
Putative methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 16S rRNA (adenine(1408)-N(1))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSivaraman, J. / Husain, N.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit.
Authors: Husain, N. / Obranic, S. / Koscinski, L. / Seetharaman, J. / Babic, F. / Bujnicki, J.M. / Maravic-Vlahovicek, G. / Sivaraman, J.
History
DepositionOct 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA methylase
B: 16S rRNA methylase
C: 16S rRNA methylase
D: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6008
Polymers103,0064
Non-polymers1,5944
Water1,33374
1
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1502
Polymers25,7511
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1502
Polymers25,7511
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1502
Polymers25,7511
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1502
Polymers25,7511
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.779, 64.419, 104.052
Angle α, β, γ (deg.)90.000, 100.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 3 / Auth seq-ID: 2 - 216 / Label seq-ID: 2 - 216

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
16S rRNA methylase


Mass: 25751.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: npmA / Production host: Escherichia coli (E. coli) / References: UniProt: A8C927
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.33 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorDate: Jun 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26821 / % possible obs: 97.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.128 / Χ2: 1.302 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.752.60.30612820.886195.2
2.75-2.82.60.27413000.98194.5
2.8-2.852.70.25313011.03195.9
2.85-2.912.70.23613571.225197.3
2.91-2.972.70.21912741.318196.6
2.97-3.042.70.20313221.476196.6
3.04-3.122.80.19113331.765196.8
3.12-3.22.80.17513091.403197.1
3.2-3.32.90.17613501.561197.8
3.3-3.42.90.17113401.353197.5
3.4-3.5230.16313291.363198.9
3.52-3.6630.16113551.378198.4
3.66-3.833.10.14413841.308198.7
3.83-4.033.10.14913391.441198.7
4.03-4.293.10.13313411.132198.6
4.29-4.623.20.1313661.211198.9
4.62-5.083.20.12213561.238198.3
5.08-5.813.20.1213941.281198.9
5.81-7.3230.09413561.328198.2
7.32-503.20.06314331.282199

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PB3

3pb3


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.825 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.534 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 2677 10.1 %RANDOM
Rwork0.252 ---
obs0.2553 26611 96.98 %-
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 max: 103.28 Å2 / Biso mean: 59.002 Å2 / Biso min: 3.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.12 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6279 0 108 74 6461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226523
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9838798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61424.247292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.654151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2371532
X-RAY DIFFRACTIONr_chiral_restr0.0960.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024828
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A784TIGHT POSITIONAL0.240.05
2B784TIGHT POSITIONAL0.240.05
3C784TIGHT POSITIONAL0.220.05
4D784TIGHT POSITIONAL0.370.05
1A779LOOSE POSITIONAL0.385
2B779LOOSE POSITIONAL0.385
3C779LOOSE POSITIONAL0.365
4D779LOOSE POSITIONAL0.595
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 179 -
Rwork0.328 1714 -
all-1893 -
obs--94.93 %
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)
10.830.29330.13411.60270.17171.0249-0.00380.0055-0.02710.1406-0.0765-0.13780.0644-0.08570.08020.0410.0101-0.04190.0640.00670.11469.95-11.6974.591
20.9525-0.8201-0.03281.5572-0.05841.53680.054-0.02390.1441-0.1132-0.1172-0.05610.11540.07570.06330.0713-0.0231-0.02110.05320.01410.058237.90912.61845.219
31.1339-0.1516-0.32571.1039-0.33221.36290.0573-0.05250.0066-0.0927-0.0681-0.04140.15490.09830.01090.09750.0462-0.02410.0289-0.01450.079755.687-14.42460.805
42.8380.09170.31442.39330.5710.28950.19070.43480.4288-0.2542-0.1818-0.6208-0.1204-0.0311-0.00890.19070.05830.08880.18380.15820.37325.39514.556-14.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 216
2X-RAY DIFFRACTION2B2 - 216
3X-RAY DIFFRACTION3C2 - 216
4X-RAY DIFFRACTION4D2 - 216

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more