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- PDB-6he1: Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O... -

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Basic information

Entry
Database: PDB / ID: 6he1
TitlePseudomonas aeruginosa 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 / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / 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)N3-methyluridine / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine--tRNA ligase
B: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,87812
Polymers94,6112
Non-polymers1,26710
Water3,117173
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-7 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.948, 121.841, 65.281
Angle α, β, γ (deg.)90.000, 113.830, 90.000
Int Tables number5
Space group name H-MC121

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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 (E. coli) / Strain (production host): Rosetta 2 (DE3) 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-FZT / 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine


Mass: 424.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N4O10S / 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.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.33 %
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-methyluridine in a solution similar to the crystallization condition but containing 22% v/v ethylene glycol.

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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: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.05→91.09 Å / Num. obs: 64736 / % possible obs: 97.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 52.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.175.81.25692880.7420.5591.37796.1
6.5-91.095.50.0320560.9990.0140.03395.4

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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
Resolution: 2.22→32.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2052 3.99 %RANDOM
Rwork0.187 ---
obs0.188 51413 97.1 %-
Displacement parametersBiso max: 177.85 Å2 / Biso mean: 58.74 Å2 / Biso min: 36.39 Å2
Baniso -1Baniso -2Baniso -3
1--4.7459 Å20 Å25.591 Å2
2---9.3005 Å20 Å2
3---14.0464 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.22→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6098 0 82 173 6353
Biso mean--52.06 58.19 -
Num. residues----801
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2167SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes941HARMONIC5
X-RAY DIFFRACTIONt_it6288HARMONIC20
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_contact7266SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6288HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8530HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion16.79
LS refinement shellResolution: 2.22→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2228 163 4.27 %
Rwork0.2047 3658 -
all0.2054 3821 -
obs--97.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.211-5.1183-0.84654.99850.30855.37320.0251-0.0759-0.51330.12440.06250.39120.68880.2371-0.08760.6069-0.00760.04970.29070.01430.3758-31.0106-30.208329.5797
20.4514-0.7012-2.3180.12260.31318.1821-0.2879-0.0699-0.19480.1047-0.09370.14370.9845-0.50140.38160.5385-0.1120.04610.681-0.07690.4227-36.308-26.937859.9936
31.25090.4748-3.08210.2975-1.32367.54380.1009-0.2120.05-0.0708-0.11950.11340.01670.09640.01860.44230.04850.05470.649-0.00250.4132-31.9822-20.41458.3072
40.57850.1654-0.19731.3967-0.10370.8165-0.09680.2201-0.0811-0.21050.1157-0.20860.20090.0506-0.01890.4675-0.0203-0.00520.5176-0.06050.4002-21.9281-12.12711.2523
51.12270.2154-0.30191.7396-0.38851.2986-0.0955-0.0486-0.05430.06140.08480.0674-0.0836-0.15760.01080.37360.0052-0.03510.4058-0.00130.3246-32.3395-4.830515.4433
60.5532-0.23540.25211.5873-0.10811.7414-0.10890.1179-0.0814-0.17470.1390.1580.1889-0.1941-0.03010.3464-0.0626-0.03860.409-0.02280.2852-34.1121-13.88586.1714
72.9237-1.18240.13921.2437-0.20512.514-0.0526-0.64010.38190.22850.2507-0.4926-0.29980.6006-0.19810.5699-0.0919-0.16420.6134-0.1260.646-4.456431.722319.6634
80.3061.0327-0.5613.9183-0.07140.9718-0.0421-0.09430.1010.31510.27230.4156-0.5029-0.231-0.23020.51140.14340.02070.58860.12370.4778-45.076129.895914.1772
90.56140.4465-0.73130.744-0.03130.4337-0.0427-0.0617-0.08550.40650.25790.48440.0767-0.6118-0.21520.40490.07210.03450.53170.0920.3916-43.86675.853122.3455
100.3663-0.4372-0.08491.0845-0.8531.6086-0.17830.17180.1353-0.06060.1462-0.0735-0.1804-0.03910.03210.362-0.0051-0.05650.37370.00650.3233-27.851211.99097.3754
110.72240.6609-0.84382.5248-0.98522.3947-0.07010.0867-0.1243-0.0070.0143-0.4267-0.06560.2760.05580.3442-0.0129-0.06710.4202-0.01030.4096-15.320111.653711.797
121.72910.0423-1.70420.7018-0.73925.5282-0.0274-0.0850.19090.19390.13280.0566-0.09440.2262-0.10540.44920.0137-0.04280.43530.01190.4197-30.976314.631116.4131
130.6597-0.1227-0.14071.31470.14291.1969-0.03270.04310.12870.07130.1071-0.0075-0.3143-0.0573-0.07440.470.0365-0.04660.44930.06670.3674-31.463426.16899.4613
142.37860.51660.11381.8891-0.2391.5140.01560.21890.0084-0.00660.1256-0.0087-0.169-0.0857-0.14120.40070.0373-0.04150.38610.04240.3127-31.700118.63666.2534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|26 }A1 - 26
2X-RAY DIFFRACTION2{ A|27 - A|64 }A27 - 64
3X-RAY DIFFRACTION3{ A|65 - A|102 }A65 - 102
4X-RAY DIFFRACTION4{ A|103 - A|166 }A103 - 166
5X-RAY DIFFRACTION5{ A|167 - A|281 }A167 - 281
6X-RAY DIFFRACTION6{ A|282 - A|426 }A282 - 426
7X-RAY DIFFRACTION7{ B|1 - B|116 }B1 - 116
8X-RAY DIFFRACTION8{ B|117 - B|138 }B117 - 138
9X-RAY DIFFRACTION9{ B|139 - B|166 }B139 - 166
10X-RAY DIFFRACTION10{ B|167 - B|213 }B167 - 213
11X-RAY DIFFRACTION11{ B|214 - B|253 }B214 - 253
12X-RAY DIFFRACTION12{ B|254 - B|281 }B254 - 281
13X-RAY DIFFRACTION13{ B|282 - B|357 }B282 - 357
14X-RAY DIFFRACTION14{ B|358 - B|426 }B358 - 426

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