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- PDB-3tqo: Structure of the cysteinyl-tRNA synthetase (cysS) from Coxiella b... -

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Basic information

Entry
Database: PDB / ID: 3tqo
TitleStructure of the cysteinyl-tRNA synthetase (cysS) from Coxiella burnetii.
ComponentsCysteinyl-tRNA synthetase
KeywordsLIGASE / Protein synthesis
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases / : / Cysteinyl-tRNA ligase anticodon binding domain / 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 ...Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases / : / Cysteinyl-tRNA ligase anticodon binding domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cysteine--tRNA ligase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8372
Polymers53,7711
Non-polymers651
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.632, 97.632, 108.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cysteinyl-tRNA synthetase / Cysteine--tRNA ligase / CysRS


Mass: 53771.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: cysS, CBU_1487 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83BL7, cysteine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: sitting drop
Details: 2 M Ammonium sulfate, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 24032 / Num. obs: 23840 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.344 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.346.60.23811660.712199.8
2.34-2.386.60.18811810.7361100
2.38-2.436.60.16711850.75199.9
2.43-2.486.50.1611750.793199.9
2.48-2.536.60.15211550.8451100
2.53-2.596.50.13211821.138199.9
2.59-2.666.50.12312061.3671100
2.66-2.736.50.12911721.794199.6
2.73-2.816.50.09811811.248199.8
2.81-2.96.50.09211691.46199.5
2.9-36.50.08211841.659199.7
3-3.126.50.07811831.444199.3
3.12-3.266.40.07112011.576199.3
3.26-3.446.40.06911721.81199.2
3.44-3.6560.06912021.618198.4
3.65-3.935.70.06811651.477196.8
3.93-4.3310.80.06811991.701198.6
4.33-4.9611.50.06412221.425199.1
4.96-6.2411.40.06812351.47199
6.24-1009.40.05413051.4195.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→36.233 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8233 / SU ML: 0.31 / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1221 5.13 %Random
Rwork0.2084 ---
all0.211 25012 --
obs0.211 23791 99.14 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.062 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 183.3 Å2 / Biso mean: 37.0129 Å2 / Biso min: 4.75 Å2
Baniso -1Baniso -2Baniso -3
1-3.8841 Å20 Å2-0 Å2
2--3.8841 Å2-0 Å2
3----7.7683 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 1 150 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033233
X-RAY DIFFRACTIONf_angle_d0.7244354
X-RAY DIFFRACTIONf_chiral_restr0.054456
X-RAY DIFFRACTIONf_plane_restr0.003563
X-RAY DIFFRACTIONf_dihedral_angle_d13.3091225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38710.27881300.20822461259199
2.3871-2.49570.26161250.209824812606100
2.4957-2.62730.28621420.209324782620100
2.6273-2.79180.28881530.206124882641100
2.7918-3.00730.29811260.216524832609100
3.0073-3.30970.27361470.21832496264399
3.3097-3.78820.25671390.23162473261298
3.7882-4.77110.21141330.17472525265898
4.7711-36.23780.26691260.21652685281198
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)
10.26850.3074-0.13120.99830.01291.05260.07610.0403-0.10370.0187-0.0583-0.12460.05750.1657-0.04290.04990.025-0.01780.1579-0.08050.096310.602223.2007-21.3138
20.95760.70980.29131.2317-0.08121.53150.11-0.27280.03020.1785-0.10610.2383-0.1167-0.02040.00010.16060.04180.04560.2321-0.0660.19492.231731.1496-6.953
30.34670.1985-0.00930.6696-0.05320.73170.0860.07310.03930.0433-0.04160.1767-0.0343-0.1425-0.0280.06830.01630.00670.1898-0.06470.16682.556529.3953-11.9982
41.32670.09180.08440.70820.18530.1807-0.02480.6012-0.1014-0.16340.1728-0.07630.03650.0629-0.11130.18570.0291-0.04580.3324-0.10.14026.687523.8527-38.7868
50.14580.267-0.34170.55510.16581.7122-0.0076-0.02730.0156-0.2550.0067-0.065-0.07010.7218-0.02660.18120.09620.01060.5278-0.09030.136727.972623.7817-42.9842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:103)A-1 - 103
2X-RAY DIFFRACTION2(chain A and resid 104:176)A104 - 176
3X-RAY DIFFRACTION3(chain A and resid 177:268)A177 - 268
4X-RAY DIFFRACTION4(chain A and resid 269:316)A269 - 316
5X-RAY DIFFRACTION5(chain A and resid 317:404)A317 - 404

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