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- PDB-3pco: crystal structure of E. coli phenylalanine-tRNA synthetase comple... -

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Basic information

Entry
Database: PDB / ID: 3pco
Titlecrystal structure of E. coli phenylalanine-tRNA synthetase complexed with phenylalanine and AMP
Components
  • Phenylalanyl-tRNA synthetase, alpha subunit
  • Phenylalanyl-tRNA synthetase, beta chain
KeywordsLIGASE / AMINOACYLATION / TRNA-BINDING / DNA-BINDING DOMAIN / FOUR-HELIX BUNDLE / AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
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
ADENOSINE MONOPHOSPHATE / PHENYLALANINE / : / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsMermershtain, I. / Finarov, I. / Klipcan, L. / Kessler, N. / Rozenberg, H. / Safro, M.G.
CitationJournal: Protein Sci. / Year: 2011
Title: Idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP.
Authors: Mermershtain, I. / Finarov, I. / Klipcan, L. / Kessler, N. / Rozenberg, H. / Safro, M.G.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phenylalanyl-tRNA synthetase, alpha subunit
B: Phenylalanyl-tRNA synthetase, beta chain
C: Phenylalanyl-tRNA synthetase, alpha subunit
D: Phenylalanyl-tRNA synthetase, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,7468
Polymers248,7224
Non-polymers1,0254
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25320 Å2
ΔGint-84 kcal/mol
Surface area87320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.547, 178.936, 254.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phenylalanyl-tRNA synthetase, alpha subunit


Mass: 36877.730 Da / Num. of mol.: 2 / Fragment: LIGASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EcDH1_1928 / Plasmid: PQE31+ / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: C9QTZ3, UniProt: P08312*PLUS
#2: Protein Phenylalanyl-tRNA synthetase, beta chain


Mass: 87483.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PQE31+ / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: P07395
#3: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine--tRNA ligase beta chain / PheRS


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / References: phenylalanine-tRNA ligase
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17%-20% PEG 8000K, 0.2 M MgCl2, 0.1 M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→38.71 Å / Num. all: 5749 / Num. obs: 58932 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.112 / Χ2: 0.934 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.113.80.80857490.79198.3
3.11-3.234.40.56558260.81899.9
3.23-3.384.60.38258460.85299.9
3.38-3.564.60.25758360.91599.8
3.56-3.784.60.18258790.93799.7
3.78-4.074.60.12758990.97399.7
4.07-4.484.50.09358620.98999.5
4.48-5.134.50.0765910199.3
5.13-6.464.50.09459881.06199
6.46-404.20.05461370.96197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry code 1PYS

1pys


Resolution: 3.02→38.71 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 0.43 / SU B: 54.147 / SU ML: 0.438 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 2981 5.1 %RANDOM
Rwork0.2317 ---
all0.2352 5749 --
obs0.2352 58880 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.12 Å2 / Biso mean: 91.794 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å20 Å2
2--1.6 Å20 Å2
3----5.13 Å2
Refinement stepCycle: LAST / Resolution: 3.02→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16654 0 70 0 16724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02217016
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.96523081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.26152153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40523.897793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.899152895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.14415147
X-RAY DIFFRACTIONr_chiral_restr0.1350.22626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112967
X-RAY DIFFRACTIONr_mcbond_it0.4861.510715
X-RAY DIFFRACTIONr_mcangle_it0.934217274
X-RAY DIFFRACTIONr_scbond_it1.28636301
X-RAY DIFFRACTIONr_scangle_it2.2614.55807
LS refinement shellResolution: 3.02→3.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 181 -
Rwork0.32 3555 -
all-3736 -
obs--85.85 %
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)
11.07560.147-0.33732.6586-0.25220.55860.10020.06020.00070.611-0.15420.15580.0422-0.08930.0540.178-0.06470.04950.0776-0.01530.0737-33.7169-6.91174.825
20.43310.0679-0.03120.7178-0.22340.69230.0461-0.00430.09980.1965-0.04690.09640.10920.01060.00080.1149-0.05670.04270.1451-0.02250.2359-33.4204-5.569174.9149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 327
2X-RAY DIFFRACTION1C86 - 327
3X-RAY DIFFRACTION2B1 - 795
4X-RAY DIFFRACTION2D1 - 795

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