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- PDB-1li7: Crystal Structure of Cysteinyl-tRNA Synthetase with Cysteine Subs... -

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Basic information

Entry
Database: PDB / ID: 1li7
TitleCrystal Structure of Cysteinyl-tRNA Synthetase with Cysteine Substrate Bound
ComponentsCYSTEINYL-TRNA SYNTHETASE
KeywordsLIGASE / TRNA SYNTHETASE / CYSTEINE / E.COLI
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 / cytosol / cytoplasm
Similarity search - Function
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases / 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 ...Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / Cysteine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsNewberry, K.J. / Hou, Y.-M. / Perona, J.J.
Citation
Journal: EMBO J. / Year: 2002
Title: Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase
Authors: Newberry, K.J. / Hou, Y.-M. / Perona, J.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary Diffraction Analysis of Escherichia Coli Cysteinyl-tRNA Synthetase
Authors: Newberry, K.J. / Kohn, J. / Hou, Y.-M. / Perona, J.J.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / struct_site
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_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.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.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_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 SYNTHETASE
B: CYSTEINYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9156
Polymers104,5422
Non-polymers3734
Water1,27971
1
A: CYSTEINYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4583
Polymers52,2711
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYSTEINYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4583
Polymers52,2711
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.980, 118.980, 143.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
DetailsThe biological unit is a monomer with one cysteine molecule bound

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Components

#1: Protein CYSTEINYL-TRNA SYNTHETASE / E.C.6.1.1.16 / Cysteine--tRNA ligase / CysRS / transfer RNA-Cys synthetase


Mass: 52271.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P21888, cysteine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.43 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 8000, 200 MM magnesium acetate, 1MM DTT, cacodylate, 5MM ATP, 10MM cysteine. 100 MM BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
210 mMHEPES1droppH7.4
350 mM1dropNaCl
41 mMdithiothreitol1drop
55 mM1dropMgCl2
65 mMATP1drop
710 mMcysteine1drop
815-17 %PEG80001reservoir
9100 mMsodium cacodylate1reservoirpH6.5
10200 mMmagnesium acetate1reservoir
112 %t-butanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 6, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→55 Å / Num. all: 32383 / Num. obs: 32373 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4634 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 55 Å / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1LI5

1li5


Resolution: 2.6→19.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2482879.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3231 10 %RANDOM
Rwork0.25 ---
all0.251 32383 --
obs0.251 32373 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.4565 Å2 / ksol: 0.317251 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 16 71 5827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 537 10.2 %
Rwork0.32 4738 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4FCY.PARFCY.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor obs: 0.249 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.97
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.31
LS refinement shell
*PLUS
Rfactor Rwork: 0.32

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