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- PDB-6ote: Crystal Structure of Seryl-tRNA synthetase (SerRS) from Cryptospo... -

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Basic information

Entry
Database: PDB / ID: 6ote
TitleCrystal Structure of Seryl-tRNA synthetase (SerRS) from Cryptosporidium parvum complexed with L-Serylsulfamoyl Adenosine
ComponentsSeryl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / SSGCID / tRNA binding / ATP binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...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) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Seryl-tRNA synthetase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Seryl-tRNA synthetase (SerRS) from Cryptosporidium parvum complexed with L-Serylsulfamoyl Adenosine
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Seryl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0853
Polymers65,6281
Non-polymers4582
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Seryl-tRNA synthetase, cytoplasmic
hetero molecules

A: Seryl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1706
Polymers131,2552
Non-polymers9154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area5980 Å2
ΔGint-44 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.210, 92.210, 257.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Seryl-tRNA synthetase, cytoplasmic


Mass: 65627.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd8_4720 / Plasmid: CrpaA.01238.a.HZ1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5CVB3
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CrpaA.01238.a.HZ1.PW38382 at 34.26 mg/ml was incubated with 3 mM Ser-AMS, then was mixed 1:1 with Wiz3/4(c4): 70% (v/v) MPD, 0.1 M HEPES / NaOH, pH = 7.5. Tray: 297963c4, puck: wuq4-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 2, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.95→44.92 Å / Num. obs: 12140 / % possible obs: 99.8 % / Redundancy: 9.246 % / Biso Wilson estimate: 67.553 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.085 / Χ2: 0.986 / Net I/σ(I): 17.83 / Num. measured all: 112243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.039.7370.5593.9584528688680.9040.59100
3.03-3.119.6790.4574.8383638648640.9220.484100
3.11-3.29.6440.3396.5880538358350.9610.359100
3.2-3.39.530.2728.2377678158150.9720.288100
3.3-3.419.4780.21610.0874027817810.9830.228100
3.41-3.539.3560.16412.571487647640.9910.173100
3.53-3.669.1970.13914.7167237317310.9930.147100
3.66-3.819.0910.10618.1964737127120.9950.112100
3.81-3.989.0470.09420.0962066866860.9970.099100
3.98-4.179.0740.08122.559716596580.9970.08699.8
4.17-4.48.9910.0712556916336330.9980.075100
4.4-4.669.1180.06428.1453255855840.9980.06799.8
4.66-4.999.1350.06629.0751435645630.9970.0799.8
4.99-5.399.0820.06428.147505245230.9970.06799.8
5.39-5.99.2170.06227.1845074904890.9970.06599.8
5.9-6.69.1630.05528.4741514544530.9980.05899.8
6.6-7.629.1290.04729.8936063963950.9990.0599.7
7.62-9.338.7710.04131.9130263473450.9990.04399.4
9.33-13.198.3490.03134.5123212802780.9990.03399.3
13.19-44.927.1470.02930.611651711630.9990.03295.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNE

3qne


Resolution: 2.95→44.92 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 718 6.1 %
Rwork0.2085 11048 -
obs0.2112 11766 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.42 Å2 / Biso mean: 73.2247 Å2 / Biso min: 27.6 Å2
Refinement stepCycle: final / Resolution: 2.95→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 30 11 3059
Biso mean--47.48 59.04 -
Num. residues----409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9502-3.17790.34411350.25422065220093
3.1779-3.49760.25341250.21672151227696
3.4976-4.00350.24161620.19982190235298
4.0035-5.04290.23151320.18092263239599
5.0429-44.92520.25381640.22342379254399
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)
11.0356-2.5412.18287.5794-5.05554.11790.12160.14150.07770.43380.33120.7546-0.2652-0.3303-0.51090.5022-0.02280.00810.57070.01590.673935.5934-9.517648.3542
22.6827-0.5124-0.03661.9380.05951.5640.08020.33630.2656-0.2802-0.225-0.2709-0.27440.20710.15950.5140.0125-0.01320.46950.10290.38989.97410.085122.208
34.5144-1.68290.91223.87310.90093.7354-0.2083-0.4336-0.59040.68740.0801-0.3409-0.23150.35480.17150.61360.0553-0.10680.49010.1170.52147.8713-0.723140.9095
42.8088-0.49870.10512.75860.09012.14220.00290.40560.1946-0.17-0.2269-0.3812-0.21750.39750.15920.4060.01540.02050.49130.09890.387815.61755.790820.5673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 110 )A3 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 218 )A111 - 218
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 250 )A219 - 250
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 446 )A251 - 446

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