[English] 日本語
Yorodumi
- PDB-5zct: The crystal structure of the poly-alpha-L-glutamate peptides synt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zct
TitleThe crystal structure of the poly-alpha-L-glutamate peptides synthetase RimK at 2.05 angstrom resolution.
ComponentsRibosomal protein S6--L-glutamate ligaseRibosome
KeywordsLIGASE / L-amino acid ligase
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ribosomal protein bS6--L-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsArimura, Y. / Kono, T. / Kino, K. / Kurumizaka, H.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structural polymorphism of the Escherichia coli poly-alpha-L-glutamate synthetase RimK
Authors: Arimura, Y. / Kono, T. / Kino, K. / Kurumizaka, H.
History
DepositionFeb 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosomal protein S6--L-glutamate ligase
B: Ribosomal protein S6--L-glutamate ligase
C: Ribosomal protein S6--L-glutamate ligase
D: Ribosomal protein S6--L-glutamate ligase
E: Ribosomal protein S6--L-glutamate ligase
F: Ribosomal protein S6--L-glutamate ligase
G: Ribosomal protein S6--L-glutamate ligase
H: Ribosomal protein S6--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,42338
Polymers264,8348
Non-polymers5,58930
Water21,3661186
1
A: Ribosomal protein S6--L-glutamate ligase
B: Ribosomal protein S6--L-glutamate ligase
C: Ribosomal protein S6--L-glutamate ligase
D: Ribosomal protein S6--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,30820
Polymers132,4174
Non-polymers2,89116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-258 kcal/mol
Surface area41960 Å2
MethodPISA
2
E: Ribosomal protein S6--L-glutamate ligase
F: Ribosomal protein S6--L-glutamate ligase
G: Ribosomal protein S6--L-glutamate ligase
H: Ribosomal protein S6--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,11518
Polymers132,4174
Non-polymers2,69814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16840 Å2
ΔGint-261 kcal/mol
Surface area42960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.618, 121.628, 119.741
Angle α, β, γ (deg.)90.000, 118.740, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Ribosomal protein S6--L-glutamate ligase / Ribosome / Polyglutamate synthase / Ribosomal protein S6 modification protein


Mass: 33104.254 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rimK, b0852, JW0836 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0C0U4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1186 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane (pH 7.0), 210 mM Na2SO4, and 16% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 164792 / % possible obs: 98.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 34.65 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.033 / Rrim(I) all: 0.08 / Χ2: 1.004 / Net I/σ(I): 7.2 / Num. measured all: 875207
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.124.10.55164180.5570.2990.6290.5998.8
2.12-2.214.70.462165820.7520.2320.5190.60599.5
2.21-2.314.10.297150810.9220.1540.3361.34490.7
2.31-2.434.90.27165620.9230.1320.3010.6999.6
2.43-2.585.40.205165890.9640.0950.2260.73899.7
2.58-2.785.60.149166750.9820.0680.1640.81999.8
2.78-3.065.60.104166080.9910.0470.1140.93799.8
3.06-3.516.20.073166800.9960.0310.081.14499.9
3.51-4.426.10.055166680.9970.0240.061.45599.6
4.42-506.40.046169290.9980.020.051.42499.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.59 Å48.21 Å
Translation8.59 Å48.21 Å

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWX

4iwx


Resolution: 2.05→48.213 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.73
RfactorNum. reflection% reflection
Rfree0.2398 8436 5.14 %
Rwork0.196 --
obs0.1983 164146 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.85 Å2 / Biso mean: 42.3758 Å2 / Biso min: 17.94 Å2
Refinement stepCycle: final / Resolution: 2.05→48.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17697 0 326 1186 19209
Biso mean--51.08 42.96 -
Num. residues----2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818265
X-RAY DIFFRACTIONf_angle_d1.06724750
X-RAY DIFFRACTIONf_chiral_restr0.0562892
X-RAY DIFFRACTIONf_plane_restr0.0063173
X-RAY DIFFRACTIONf_dihedral_angle_d10.77611111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07330.33052720.28714957522994
2.0733-2.09770.32092820.28355201548399
2.0977-2.12330.31062920.26585195548799
2.1233-2.15020.28232880.24525287557599
2.1502-2.17850.29722700.243952535523100
2.1785-2.20830.27542790.241552195498100
2.2083-2.23990.48742760.38954399467585
2.2399-2.27330.56952190.51024078429777
2.2733-2.30880.28462810.2255248552999
2.3088-2.34670.2622930.22215243553699
2.3467-2.38710.2892750.217752315506100
2.3871-2.43060.27882730.215352985571100
2.4306-2.47730.27622600.211352595519100
2.4773-2.52790.25962900.20551935483100
2.5279-2.58280.25212730.204452965569100
2.5828-2.64290.26673150.204352455560100
2.6429-2.7090.24552840.197152995583100
2.709-2.78220.25872940.202652765570100
2.7822-2.86410.25442650.218352235488100
2.8641-2.95650.28632690.215253035572100
2.9565-3.06220.27352870.207352955582100
3.0622-3.18480.26413050.206552515556100
3.1848-3.32970.25163170.201652535570100
3.3297-3.50520.233040.190552645568100
3.5052-3.72470.25032860.18955239552599
3.7247-4.01220.19432820.171352785560100
4.0122-4.41570.17683140.149752815595100
4.4157-5.0540.17832640.146153605624100
5.054-6.36520.19752600.173453605620100
6.3652-48.22660.16632670.151954265693100

+
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