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- PDB-3ica: The crystal structure of the beta subunit of a phenylalanyl-tRNA ... -

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Basic information

Entry
Database: PDB / ID: 3ica
TitleThe crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from Porphyromonas gingivalis W83
ComponentsPhenylalanyl-tRNA synthetase beta chain
KeywordsLIGASE / APC61692.1 / Porphyromonas gingivalis / phenylalanyl-tRNA synthetase / beta subunit / Structural genomics / PSI-2 / Protein structure initiative / Midwest Center for Structural Genomics / MCSG / Aminoacyl-tRNA synthetase / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Protein biosynthesis / RNA-binding / tRNA-binding
Function / homology
Function and homology information


phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / 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 ...Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / 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 / Phenylalanine-tRNA ligase, class IIc, beta subunit / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / 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 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phenylalanine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å
AuthorsFan, Y. / Sather, A. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from Porphyromonas gingivalis W83
Authors: Fan, Y. / Sather, A. / Keigher, L. / Joachimiak, A.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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 / 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.pdbx_leaving_atom_flag / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,24414
Polymers49,0682
Non-polymers1,17612
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-21 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.725, 59.725, 256.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 24534.096 Da / Num. of mol.: 2 / Fragment: sequence database residues 503-712
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0099, pheT, Porphyromonas gingivalis / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q7MXR4, phenylalanine-tRNA ligase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris pH8.5, 30% v/v PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 18220 / % possible obs: 99.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 32.553
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.214 / Num. unique all: 859 / % possible all: 93.3

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
SHELXDphasing
MLPHAREphasing
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.44→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.568 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.289
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25486 891 4.9 %RANDOM
Rwork0.20248 ---
obs0.20505 17329 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2--1.98 Å20 Å2
3----3.97 Å2
Refinement stepCycle: LAST / Resolution: 2.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 77 161 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223505
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9724724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25623.494166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71915606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7421528
X-RAY DIFFRACTIONr_chiral_restr0.0880.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022608
X-RAY DIFFRACTIONr_mcbond_it0.8691.52086
X-RAY DIFFRACTIONr_mcangle_it1.66823350
X-RAY DIFFRACTIONr_scbond_it2.24631419
X-RAY DIFFRACTIONr_scangle_it3.6554.51374
LS refinement shellResolution: 2.44→2.505 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 58 -
Rwork0.258 1259 -
obs--99.85 %

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