[English] 日本語
Yorodumi
- PDB-6hhy: Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hhy
TitleKlebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine
ComponentsSerine--tRNA ligase
KeywordsLIGASE / Coil-coil / Beta barrel / tRNA synthetase / Inhibitor / Complex
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPang, L. / De Graef, S. / Weeks, S.D. / Strelkov, S.V.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
Research Foundation - Flanders1S53516N Belgium
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.3Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4008
Polymers48,6691
Non-polymers7317
Water1,53185
1
A: Serine--tRNA ligase
hetero molecules

A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,80016
Polymers97,3382
Non-polymers1,46214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6870 Å2
ΔGint-42 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.721, 83.721, 228.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Serine--tRNA ligase / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 48669.180 Da / Num. of mol.: 1 / Fragment: Seryl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: serS, AGG09_05015, B1727_25560, B4U21_07300, B4U22_08075, BB785_18280, BL124_0015080, BN49_2024, C3483_17160, C3F39_05595, C9J88_18700, CPT10_05250, CSC88_02630, CWQ24_18365, PMK1_03261, SM57_00973
Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS
References: UniProt: W9BNU9, UniProt: A6T6Z0*PLUS, serine-tRNA ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FZT / 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine


Mass: 424.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N4O10S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus ...Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus buffer system 1 (MES/Imidazole) pH 6.5. Suitable crystals were soaked with 2 mM compound in a similar crystallization solution containing a 10% w/v PEG 8000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.98→76.14 Å / Num. obs: 57726 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 57.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Rrim(I) all: 0.089 / Net I/σ(I): 12.1 / Num. measured all: 497991
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.98-2.099.12.33982510.7120.8172.4899.8
6.26-76.147.40.03220870.9990.0120.035100

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
PHASER1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model generated from structure 2DQ3

2dq3


Resolution: 2.27→67.52 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1950 5.06 %RANDOM
Rwork0.213 ---
obs0.214 38511 100 %-
Displacement parametersBiso max: 168.94 Å2 / Biso mean: 60.09 Å2 / Biso min: 35.32 Å2
Baniso -1Baniso -2Baniso -3
1--8.9464 Å20 Å20 Å2
2---8.9464 Å20 Å2
3---17.8928 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.27→67.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 43 85 3426
Biso mean--55.05 57.32 -
Num. residues----424
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1213SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes502HARMONIC5
X-RAY DIFFRACTIONt_it3401HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion442SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3776SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3401HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4604HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion16.91
LS refinement shellResolution: 2.27→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2231 143 4.91 %
Rwork0.2248 2771 -
all0.2247 2914 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: -11.5872 Å / Origin y: -31.0369 Å / Origin z: -9.7036 Å
111213212223313233
T-0.0701 Å20.0471 Å2-0.0116 Å2--0.0702 Å20.0442 Å2---0.1236 Å2
L0.4251 °20.1137 °20.0505 °2-0.2973 °20.4012 °2--1.2879 °2
S0.0332 Å °-0.0427 Å °-0.0426 Å °-0.0567 Å °-0.0484 Å °-0.0602 Å °0.0626 Å °0.3265 Å °0.0152 Å °
Refinement TLS groupSelection details: {A|*}

+
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