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- PDB-2rhq: PheRS from Staphylococcus haemolyticus- rational protein engineer... -

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Basic information

Entry
Database: PDB / ID: 2rhq
TitlePheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies
Components
  • Phenylalanyl-tRNA synthetase alpha chain
  • Phenylalanyl-tRNA synthetase beta chain
KeywordsLIGASE / heterotetramer / phenylalanine / tRNA / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Magnesium / Metal-binding / Nucleotide-binding / Protein biosynthesis / RNA-binding / tRNA-binding
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / transferase activity / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain ...Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-GAX / Phenylalanine--tRNA ligase alpha subunit / Phenylalanine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesStaphylococcus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsEvdokimov, A.G. / Mekel, M.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Rational protein engineering in action: the first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus.
Authors: Evdokimov, A.G. / Mekel, M. / Hutchings, K. / Narasimhan, L. / Holler, T. / McGrath, T. / Beattie, B. / Fauman, E. / Yan, C. / Heaslet, H. / Walter, R. / Finzel, B. / Ohren, J. / McConnell, ...Authors: Evdokimov, A.G. / Mekel, M. / Hutchings, K. / Narasimhan, L. / Holler, T. / McGrath, T. / Beattie, B. / Fauman, E. / Yan, C. / Heaslet, H. / Walter, R. / Finzel, B. / Ohren, J. / McConnell, P. / Braden, T. / Sun, F. / Spessard, C. / Banotai, C. / Al-Kassim, L. / Ma, W. / Wengender, P. / Kole, D. / Garceau, N. / Toogood, P. / Liu, J.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1134
Polymers121,6032
Non-polymers5102
Water6,287349
1
A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules

A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,2268
Polymers243,2064
Non-polymers1,0204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.312, 87.602, 61.072
Angle α, β, γ (deg.)90.000, 100.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phenylalanyl-tRNA synthetase alpha chain / Phenylalanine--tRNA ligase alpha chain / PheRS


Mass: 33395.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Gene: pheS / Plasmid: pET15 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL-AI / References: UniProt: Q4L5E3, phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA synthetase beta chain / Phenylalanine--tRNA ligase beta chain / PheRS


Mass: 88207.195 Da / Num. of mol.: 1 / Mutation: D34N, D58G, A59S, D60G, Q144P, Q795E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Gene: pheT / Plasmid: pET15 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL-AI / References: UniProt: Q4L5E4, phenylalanine-tRNA ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GAX / 1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea


Mass: 444.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N6O3S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG3350, 0.4M sodium formate, 0.1M Bis-Tris propane, pH 6.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 10, 2006 / Details: Si monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→35.6 Å / Num. all: 62893 / Num. obs: 62893 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.91
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.16 / Num. unique all: 6217 / % possible all: 76.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 2.2→35.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.754 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3192 5.1 %RANDOM
Rwork0.196 ---
obs0.2 62889 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.193 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å2-0.73 Å2
2--2.91 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 31 349 8715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228516
X-RAY DIFFRACTIONr_bond_other_d00.027739
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.97311531
X-RAY DIFFRACTIONr_angle_other_deg0.745318066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.73451065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08425.074406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.078151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8311551
X-RAY DIFFRACTIONr_chiral_restr0.1090.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029491
X-RAY DIFFRACTIONr_gen_planes_other00.021617
X-RAY DIFFRACTIONr_nbd_refined0.2350.31825
X-RAY DIFFRACTIONr_nbd_other0.2460.38263
X-RAY DIFFRACTIONr_nbtor_refined0.1930.54070
X-RAY DIFFRACTIONr_nbtor_other0.0990.54973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.5639
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1710.58
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.3160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.530
X-RAY DIFFRACTIONr_mcbond_it3.5281.56691
X-RAY DIFFRACTIONr_mcbond_other1.0331.52165
X-RAY DIFFRACTIONr_mcangle_it4.33928552
X-RAY DIFFRACTIONr_scbond_it6.48633662
X-RAY DIFFRACTIONr_scangle_it8.5154.52973
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 189 -
Rwork0.265 3336 -
all-3525 -
obs--72.83 %

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