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- PDB-3sp1: Crystal structure of cysteinyl-tRNA synthetase (cysS) from Borrel... -

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Basic information

Entry
Database: PDB / ID: 3sp1
TitleCrystal structure of cysteinyl-tRNA synthetase (cysS) from Borrelia burgdorferi
ComponentsCysteinyl-tRNA synthetase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / lyme disease / peptide synthesis / protein biosynthesis / tRNA / CysRS / Cysteine tRNA ligase
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Cysteine-tRNA ligase, C-terminal anti-codon recognition domain / 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 ...Cysteine-tRNA ligase, C-terminal anti-codon recognition domain / 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
ADENOSINE MONOPHOSPHATE / Cysteine--tRNA ligase
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2017
Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.
Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 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_ncs_dom_lim / 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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: Cysteinyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6367
Polymers116,7752
Non-polymers8615
Water2,882160
1
A: Cysteinyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8003
Polymers58,3881
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cysteinyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8364
Polymers58,3881
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.620, 49.890, 179.630
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 2 - 468 / Label seq-ID: 23 - 489

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 58387.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_0599, cysS / Production host: Escherichia coli (E. coli) / References: UniProt: O51545, 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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein at 25 mg/mL against PACT E9 25% PEG 3350, 0.2 M Na K Tartrate with 25% ethylene glycol as cryo-protectant, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 36778 / Num. obs: 36598 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.48
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.55-2.620.5242.52199
2.62-2.690.4942.91199.7
2.69-2.770.3843.72199.7
2.77-2.850.3224.61199.6
2.85-2.940.2655.571100
2.94-3.050.2246.56199.7
3.05-3.160.1817.981100
3.16-3.290.1429.781100
3.29-3.440.11712.22199.9
3.44-3.610.09714.661100
3.61-3.80.0817.62199.7
3.8-4.030.06320.83199.9
4.03-4.310.05622.77199.9
4.31-4.660.04825.79199.9
4.66-5.10.05224.261100
5.1-5.70.06419.82199.7
5.7-6.580.07418.64199.8
6.58-8.060.05323.03199.7
8.06-11.40.03136.84199.9
11.40.03437.12178.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.45 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.93 Å
Translation3 Å19.93 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LI5

1li5


Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.334 / SU ML: 0.236 / SU R Cruickshank DPI: 0.607 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27398 1835 5 %RANDOM
Rwork0.22433 ---
obs0.2268 34652 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.11 Å2
2--1.18 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 49 160 7017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027018
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9459522
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24724.227343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.832151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.651527
X-RAY DIFFRACTIONr_chiral_restr0.110.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025358
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6281.54253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.226784
X-RAY DIFFRACTIONr_scbond_it1.74132764
X-RAY DIFFRACTIONr_scangle_it2.8034.52737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3277 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.295
LOOSE THERMAL1.5910
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 136 -
Rwork0.304 2439 -
obs--98.81 %
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)
10.78040.8964-0.47781.2447-0.06471.40750.0804-0.03810.03850.1815-0.05950.02250.1613-0.0116-0.0210.0494-0.01860.00820.0427-0.00170.1035-13.46763.6959-77.1531
20.31930.1269-0.47670.53690.43531.5690.06220.01190.07420.14740.0598-0.0180.10190.0292-0.1220.07070.01180.0170.051-0.02370.0735-12.04467.3114-64.3951
31.20870.11981.00290.63050.14670.85350.10860.09410.03490.0129-0.12430.00670.12520.07840.01570.0830.01910.01090.0795-0.01990.0417-10.6437-5.1774-98.9594
40.7266-0.77851.13341.5887-1.10111.91290.05260.04920.048-0.2043-0.2136-0.1514-0.0570.05540.1610.12080.0307-0.03460.06410.0180.0936-16.05969.6878-116.3753
50.9402-1.28030.6771.7787-1.06941.36860.04360.0799-0.0543-0.0094-0.10510.0292-0.30010.07230.06140.13380.0069-0.0260.0437-0.0180.0883-18.372531.8462-12.7841
60.15310.07460.42660.28520.15341.52210.0170.0192-0.042-0.05270.0377-0.0732-0.06850.0195-0.05470.06910.0221-0.00140.0666-0.01010.0662-14.70124.6262-19.8894
71.5943-0.186-0.67290.5875-0.68372.04370.135-0.1511-0.0363-0.0309-0.0980.0885-0.1760.0254-0.0370.0420.0212-0.00590.097-0.04710.0529-20.26737.746913.3004
80.82121.22-0.99362.134-1.49521.20450.0876-0.15990.00170.1461-0.09610.053-0.0930.18270.00850.0789-0.0738-0.00460.16010.0280.0202-20.769121.244226.6346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2A101 - 295
3X-RAY DIFFRACTION3A296 - 409
4X-RAY DIFFRACTION4A410 - 469
5X-RAY DIFFRACTION5B1 - 46
6X-RAY DIFFRACTION6B47 - 328
7X-RAY DIFFRACTION7B329 - 408
8X-RAY DIFFRACTION8B409 - 469

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