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- PDB-6rlu: Trypanosoma brucei Seryl-tRNA Synthetase in Complex with 5'-O-(N-... -

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Basic information

Entry
Database: PDB / ID: 6rlu
TitleTrypanosoma brucei Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine
ComponentsSeryl-tRNA synthetase, putative
KeywordsLIGASE / Coil-coil / Beta barrel / tRNA synthetase / Inhibitor / Complex
Function / homology
Function and homology information


serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / ATP binding
Similarity search - Function
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) / 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)
Similarity search - Domain/homology
5'-O-(N-(L-seryl)-sulfamoyl)cytidine / MALONATE ION / serine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 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
DepositionMay 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seryl-tRNA synthetase, putative
B: Seryl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,73420
Polymers107,8462
Non-polymers1,88818
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-85 kcal/mol
Surface area37930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.357, 178.357, 246.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Seryl-tRNA synthetase, putative


Mass: 53923.203 Da / Num. of mol.: 2 / Fragment: Seryl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote)
Gene: TbgDal_XI8110 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: D0A7P1, serine-tRNA ligase

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Non-polymers , 5 types, 792 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, 5% (v/v) glycerol was mixed with 2.4 M sodium malonate pH 7.0, 100 mM Bis-tris propane pH 7.0 in a 2:1 (v/v) ratio. ...Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, 5% (v/v) glycerol was mixed with 2.4 M sodium malonate pH 7.0, 100 mM Bis-tris propane pH 7.0 in a 2:1 (v/v) ratio. Suitable crystals were soaked with 2 mM 5'-O-(N-(L-seryl)-sulfamoyl)cytidine in t crystallization solution containing a 22% v/v glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.88→96.38 Å / Num. obs: 121071 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 25.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.035 / Rrim(I) all: 0.115 / Net I/σ(I): 15.5 / Num. measured all: 1319265 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.88-1.9910.80.722188992175200.8940.2290.7583.4100
5.96-96.3810.60.044256740250.9990.0130.04239.699.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LSQ

3lsq


Resolution: 1.88→27.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2321 1.92 %RANDOM
Rwork0.169 ---
obs0.169 121020 100 %-
Displacement parametersBiso max: 113.15 Å2 / Biso mean: 30.33 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.7158 Å20 Å20 Å2
2---1.7158 Å20 Å2
3---3.4315 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.88→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7099 0 121 776 7996
Biso mean--33.28 42.79 -
Num. residues----922
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2594SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1266HARMONIC5
X-RAY DIFFRACTIONt_it7341HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion971SEMIHARMONIC5
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_contact9196SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7341HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg9914HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion14.7
LS refinement shellResolution: 1.88→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.218 47 1.94 %
Rwork0.1904 2374 -
all0.1909 2421 -
obs--100 %
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)
13.99890.6383.01861.16891.57935.61440.2087-0.4895-0.30080.0949-0.08580.05010.3101-0.6686-0.12280.1508-0.0892-0.02350.43410.03490.191524.9009-85.439739.0682
24.26290.98073.81850.05840.95134.75810.1684-0.4906-0.31580.07960.0286-0.13420.0709-0.0878-0.1970.17090.0059-0.02810.35230.03060.20436.4031-83.768920.3686
34.35770.83492.5570.82620.40422.1981-0.0282-0.46710.01190.1168-0.0343-0.0329-0.0859-0.17070.06250.13260.00510.01850.2723-0.00770.1426-1.0672-79.498716.2034
43.51441.68770.99930.77730.37912.38660.1659-0.5582-0.03670.0526-0.16140.0760.1012-0.4817-0.00450.1902-0.0737-0.01950.23850.00410.141642.4327-82.093546.6189
50.3562-0.00960.01080.37340.01040.64870.03250.00470.02520.06340.00130.011-0.0047-0.035-0.03370.1173-0.0095-0.00080.12440.00570.137755.8861-65.246929.9863
60.97191.00320.50961.86530.22531.02750.04810.017-0.05190.0131-0.03570.16060.1168-0.2138-0.01240.0807-0.0373-0.00160.16090.0020.120640.3624-73.959523.0669
71.0241.11750.41732.6180.48641.13930.0971-0.0890.00350.1082-0.05030.07410.0373-0.1982-0.04690.1023-0.00980.00330.16050.01960.108346.6442-71.196732.5984
81.46490.37640.63020.1709-0.0920.95950.0396-0.15330.00390.0434-0.0410.00880.1239-0.16630.00150.1597-0.0341-0.02690.15460.00590.144648.9402-79.839838.5596
90.63620.85181.05040.91160.97481.29650.1625-0.1578-0.07290.0671-0.1220.01650.1802-0.238-0.04050.1478-0.0487-0.03380.15980.00250.14843.6069-81.585427.9816
100.7542-0.8528-0.91442.49682.11364.04760.0339-0.04440.12130.12850.0777-0.3021-0.0530.3896-0.11150.1258-0.016-0.04050.1925-0.01290.197872.5938-66.166832.7516
110.3629-0.5588-0.70660.97830.87471.97870.16980.14780.033-0.1342-0.08410.0495-0.5314-0.4131-0.08570.28620.08370.02260.2480.04450.210247.8724-20.491915.056
120.32980.0845-0.02960.35550.03570.4675-0.01640.04440.0172-0.0360.03690.0329-0.0367-0.0079-0.02050.0898-0.0196-0.00950.14430.00350.133158.4916-57.53589.7686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|27 }A1 - 27
2X-RAY DIFFRACTION2{ A|28 - A|67 }A28 - 67
3X-RAY DIFFRACTION3{ A|68 - A|135 }A68 - 135
4X-RAY DIFFRACTION4{ A|136 - A|160 }A136 - 160
5X-RAY DIFFRACTION5{ A|161 - A|239 }A161 - 239
6X-RAY DIFFRACTION6{ A|240 - A|294 }A240 - 294
7X-RAY DIFFRACTION7{ A|295 - A|328 }A295 - 328
8X-RAY DIFFRACTION8{ A|329 - A|399 }A329 - 399
9X-RAY DIFFRACTION9{ A|400 - A|440 }A400 - 440
10X-RAY DIFFRACTION10{ A|441 - A|465 }A441 - 465
11X-RAY DIFFRACTION11{ B|1 - B|160 }B1 - 160
12X-RAY DIFFRACTION12{ B|161 - B|465 }B161 - 465

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