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- PDB-1u0b: Crystal structure of cysteinyl-tRNA synthetase binary complex wit... -

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Basic information

Entry
Database: PDB / ID: 1u0b
TitleCrystal structure of cysteinyl-tRNA synthetase binary complex with tRNACys
Components
  • Cysteine--tRNA ligase
  • cysteinyl tRNA
KeywordsLIGASE/RNA / protein-RNA complex / LIGASE-RNA complex
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / aminoacyl-tRNA ligase activity / ligase activity / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cysteinyl-tRNA synthetase, class Ia, DALR / DALR domain / DALR_2 / Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Cysteinyl-tRNA synthetase, class Ia, DALR / DALR domain / DALR_2 / Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Cysteine--tRNA ligase / Cysteine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHauenstein, S. / Zhang, C.M. / Hou, Y.M. / Perona, J.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Shape-selective RNA recognition by cysteinyl-tRNA synthetase
Authors: Hauenstein, S. / Zhang, C.M. / Hou, Y.M. / Perona, J.J.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_keywords / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _entity_src_gen.entity_id / _entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.entity_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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_label_seq_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cysteinyl tRNA
B: Cysteine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1163
Polymers76,0502
Non-polymers651
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.490, 129.490, 91.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain cysteinyl tRNA


Mass: 23779.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 transcription / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1845826323
#2: Protein Cysteine--tRNA ligase / Cysteinyl-tRNA synthetase / CysRS


Mass: 52271.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: T7 transcription / Gene: cysS / Plasmid: pKK107 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: A0A094VYY4, UniProt: P21888*PLUS, cysteine-tRNA ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium Sulfate, PEG 1000, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 24, 2004 / Details: collimating mirror
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.86 Å / Num. all: 34495 / Num. obs: 31401 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 33.6
Reflection shellResolution: 2.3→2.41 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 4.08 / Num. unique all: 3292 / % possible all: 96.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LI5

1li5


Resolution: 2.3→24.91 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1578 5 %RANDOM
Rwork0.233 ---
all0.29 34799 --
obs0.25 31401 90.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 37.3243 Å2 / ksol: 0.353855 e/Å3
Displacement parametersBiso mean: 42.37 Å2
Baniso -1Baniso -2Baniso -3
1--7.56 Å20 Å20 Å2
2---7.56 Å20 Å2
3---15.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 1576 1 104 5199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg20.2
X-RAY DIFFRACTIONx_torsion_impr_deg1.12
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.3-2.410.3391795.20.29532640.02580.5
2.41-2.530.30818650.26935570.02387.7
2.53-2.690.3121995.10.25436840.02289.9
2.69-2.90.3031975.10.24537020.02291
2.9-3.190.3281834.50.2638530.02493.2
3.19-3.650.2942004.90.23238620.02193.3
3.65-4.60.252285.50.21238880.01793.7
4.6-24.910.2442064.90.21540130.01791.8

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