[English] 日本語
Yorodumi
- PDB-4iwy: SeMet-substituted RimK structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iwy
TitleSeMet-substituted RimK structure
ComponentsRibosomal protein S6 modification protein
KeywordsLIGASE / ATP-grasp fold
Function / homology
Function and homology information


ribosomal S6-glutamic acid ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / SOS response / protein modification process / translation / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S6--L-glutamate ligase RimK / RimK, PreATP-grasp domain / RimK PreATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 ...Ribosomal protein S6--L-glutamate ligase RimK / RimK, PreATP-grasp domain / RimK PreATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GLUTAMIC ACID / Ribosomal protein bS6--L-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsShi, D. / Zhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M.
CitationJournal: Proteins / Year: 2013
Title: Structure and function of Escherichia coli RimK, an ATP-grasp fold, l-glutamyl ligase enzyme.
Authors: Zhao, G. / Jin, Z. / Wang, Y. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosomal protein S6 modification protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2249
Polymers35,0731
Non-polymers1,1518
Water181
1
A: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,89536
Polymers140,2924
Non-polymers4,60332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area19430 Å2
ΔGint-405 kcal/mol
Surface area42640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.030, 129.030, 171.238
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-408-

SO4

-
Components

#1: Protein Ribosomal protein S6 modification protein


Mass: 35072.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0852, JW0836, rimK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C0U4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 5.87 Å3/Da / Density % sol: 79.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, and 1.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.5

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97921, 0.97934, 0.97471
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979341
30.974711
ReflectionResolution: 2.9→50 Å / Num. all: 19373 / Num. obs: 18059 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Rmerge(I) obs: 0.126 / Χ2: 1.264 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.957.70.8034950.854153.5
2.95-38.80.7286310.898166
3-3.069.70.6177300.893176.8
3.06-3.12110.6887880.899184.7
3.12-3.19120.6378630.953191.9
3.19-3.2713.50.5559070.914196.3
3.27-3.3515.10.4659490.958199.8
3.35-3.4416.20.3779531.036199.6
3.44-3.54170.3339341.046199.8
3.54-3.6517.30.2729551.108199.8
3.65-3.7817.90.2089561.152199.9
3.78-3.94180.1699531.232199.8
3.94-4.1118.10.1329561.327199.8
4.11-4.33180.1059641.452199.8
4.33-4.6180.0949761.419199.8
4.6-4.9617.80.0889711.482199.8
4.96-5.4617.60.0919801.4571100
5.46-6.2417.40.1059911.627199.9
6.24-7.8617.10.0810171.6821100
7.86-5015.60.05310901.546197.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→26.558 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.7869 / SU ML: 0.34 / σ(F): 1.34 / σ(I): 0 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1621 5 %Random
Rwork0.2049 ---
obs0.2072 18059 91.72 %-
all-35349 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.83 Å2 / Biso mean: 79.8256 Å2 / Biso min: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→26.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 67 1 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112349
X-RAY DIFFRACTIONf_angle_d1.5893186
X-RAY DIFFRACTIONf_chiral_restr0.099366
X-RAY DIFFRACTIONf_plane_restr0.008407
X-RAY DIFFRACTIONf_dihedral_angle_d17.636886
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.899-2.98420.3459740.3191413148750
2.9842-3.08040.32691040.30431931203570
3.0804-3.19030.31991290.30042385251486
3.1903-3.31780.33751460.27992730287697
3.3178-3.46850.2931450.252627752920100
3.4685-3.65090.31171490.226527942943100
3.6509-3.8790.26551420.208327852927100
3.879-4.17750.24741450.194827882933100
4.1775-4.59590.20141530.157928032956100
4.5959-5.25650.20931460.16327872933100
5.2565-6.60570.26991470.218328092956100
6.6057-26.5590.21251410.180428012942100
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)
13.5408-2.43050.69763.5171-0.20573.4585-0.0971-0.2920.04940.05340.226-0.0433-0.18010.2034-0.12630.3807-0.0144-0.00060.4514-0.00160.3815-18.676874.009273.6544
24.5911-1.5221.28145.4357-0.80464.0750.1177-0.5821-0.1639-0.4703-0.0845-0.2824-0.4310.54450.03330.6564-0.05110.03350.61130.01490.5479-3.5555.688859.8972
32.54292.6485-0.1833.99360.07125.15670.09570.2473-0.185-0.43780.30260.13640.06560.1374-0.35930.45440.0054-0.05190.3492-0.03690.5126-14.888842.482154.7934
40.8133-0.8186-0.61692.33611.09192.93080.0673-0.1173-0.21940.00790.00430.12120.4483-0.1715-0.0960.4854-0.0233-0.10080.74770.02520.579-6.300451.241975.0353
56.59841.0898-1.64846.5723-0.78525.5082-0.22650.2183-0.0310.22310.593-0.8698-0.3870.3057-0.39630.54910.0129-0.08280.6661-0.13750.6165-6.183971.758281.885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:99)A-1 - 99
2X-RAY DIFFRACTION2(chain A and resid 100:115)A100 - 115
3X-RAY DIFFRACTION3(chain A and resid 116:180)A116 - 180
4X-RAY DIFFRACTION4(chain A and resid 181:276)A181 - 276
5X-RAY DIFFRACTION5(chain A and resid 277:292)A277 - 292

+
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://pdbjlvh1.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