[English] 日本語
Yorodumi
- PDB-6he3: Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6he3
TitlePseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine
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 / 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)cytidine / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPang, L. / De Graef, S. / Strelkov, S.V. / Weeks, S.D.
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 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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: Serine--tRNA ligase
B: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,84812
Polymers94,6112
Non-polymers1,23710
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-6 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.006, 122.183, 65.489
Angle α, β, γ (deg.)90.000, 114.670, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 47305.516 Da / Num. of mol.: 2 / Fragment: Seryl-tRNA Synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: serS, ALP65_01227 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS
References: UniProt: A0A3P3Q1W7, UniProt: Q9I0M6*PLUS, serine-tRNA ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FZQ / 5'-O-(N-(L-seryl)-sulfamoyl)cytidine


Mass: 409.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N5O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5mM DTT, was mixed with an equal volume of 100 mM Tris pH 8, 200 mM NaCl, 23% w/v PEG 3350 and 5% v/v ethylene glycol. ...Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5mM DTT, was mixed with an equal volume of 100 mM Tris pH 8, 200 mM NaCl, 23% w/v PEG 3350 and 5% v/v ethylene glycol. Suitable crystals were soaked with 2 mM 5'-O-(N-(L-seryl)-sulfamoyl)N3-cytidine in a solution similar to the crystallization condition but containing 22% v/v ethylene glycol.

-
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: 2.1→91.25 Å / Num. obs: 62738 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 11.7 / Num. measured all: 214186 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.213.50.60591700.7520.3740.71399.5
6.63-91.253.30.0320350.9980.0190.03699.1

-
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 using 2DQ3 as a template

2dq3


Resolution: 2.16→43.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2239 3.91 %RANDOM
Rwork0.187 ---
obs0.188 57272 99.1 %-
Displacement parametersBiso max: 240.51 Å2 / Biso mean: 52.69 Å2 / Biso min: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1--8.9641 Å20 Å22.1753 Å2
2--4.0054 Å20 Å2
3---4.9586 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.16→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 80 343 6512
Biso mean--42.88 56.91 -
Num. residues----799
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2179SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes157HARMONIC2
X-RAY DIFFRACTIONt_gen_planes943HARMONIC5
X-RAY DIFFRACTIONt_it6295HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
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_contact7457SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6295HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8540HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion16.19
LS refinement shellResolution: 2.16→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2246 145 3.44 %
Rwork0.1986 4067 -
all0.1995 4212 -
obs--99.46 %
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)
1-0.06480.167-0.10170.3936-0.60080.74990.0063-0.0901-0.002-0.1052-0.01590.07410.1512-0.07070.00960.37340.0181-0.00660.48180.01650.364-34.1527-25.09851.5844
20.41840.26860.16272.1722-0.25820.8771-0.1360.1305-0.0777-0.27940.141-0.37930.17050.0731-0.0050.2768-0.01060.04190.3286-0.05120.3409-22.3361-12.18430.8152
31.08490.1886-0.29812.1991-0.37541.3238-0.0776-0.0686-0.08110.18030.0616-0.0007-0.0545-0.08890.01590.27360.0087-0.02830.2811-0.00230.2933-31.8804-5.000715.0247
40.51030.07630.12582.06780.06381.2076-0.08690.038-0.0642-0.11110.09980.10480.1445-0.1346-0.01290.2795-0.0542-0.01990.3334-0.01140.3062-34.5379-13.80436.0017
53.7233-0.8003-2.905300.51963.2380.3161-1.32540.57140.29670.1518-0.8783-0.82480.9973-0.46790.6059-0.1552-0.17990.7394-0.22260.9632-2.787933.923319.5821
65.4760.619-1.13950.58940.82551.9498-0.1116-1.0178-0.13340.310.2943-0.6835-0.37130.5065-0.18270.4177-0.1333-0.14220.4765-0.12250.6034-5.634328.526218.7769
70.4094-0.0649-0.04991.8157-0.44460.8214-0.0258-0.03680.04430.2490.12840.164-0.1756-0.1374-0.10260.290.049-0.01090.32230.01010.2805-36.712314.710913.2071
82.08590.8077-0.78392.2004-0.53371.83940.0449-0.1085-0.01420.2212-0.0007-0.3266-0.14530.1174-0.04420.27180.013-0.09450.2804-0.00980.3532-21.453912.735813.8423
90.8909-0.22090.11761.7533-0.13341.01890.03950.03240.09190.07380.06830.008-0.2475-0.071-0.10780.28220.0441-0.01990.26570.03590.2682-31.505122.69697.6942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|102 }A1 - 102
2X-RAY DIFFRACTION2{ A|103 - A|166 }A103 - 166
3X-RAY DIFFRACTION3{ A|167 - A|281 }A167 - 281
4X-RAY DIFFRACTION4{ A|282 - A|426 }A282 - 426
5X-RAY DIFFRACTION5{ B|1 - B|42 }B1 - 42
6X-RAY DIFFRACTION6{ B|43 - B|116 }B43 - 116
7X-RAY DIFFRACTION7{ B|117 - B|213 }B117 - 213
8X-RAY DIFFRACTION8{ B|214 - B|281 }B214 - 281
9X-RAY DIFFRACTION9{ B|282 - B|426 }B282 - 426

+
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