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- PDB-3wnd: Crystal structure of EF-Pyl -

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Basic information

Entry
Database: PDB / ID: 3wnd
TitleCrystal structure of EF-Pyl
ComponentsProtein translation elongation factor 1A
KeywordsTRANSLATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / tRNA / elongation factor / pyrrolysine
Function / homology
Function and homology information


translation elongation factor activity
Similarity search - Function
: / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Protein translation elongation factor 1A
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYanagisawa, T. / Ishii, R. / Fukunaga, R. / Sengoku, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J. Struct. Funct. Genomics / Year: 2015
Title: A SelB/EF-Tu/aIF2 gamma-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.).
Authors: Yanagisawa, T. / Ishii, R. / Hikida, Y. / Fukunaga, R. / Sengoku, T. / Sekine, S. / Yokoyama, S.
History
DepositionDec 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Protein translation elongation factor 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8783
Polymers40,4931
Non-polymers3842
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.873, 108.608, 58.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-581-

HOH

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Components

#1: Protein Protein translation elongation factor 1A / Translation factor EF-Pyl


Mass: 40493.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: JCM9314 / Gene: MM_1309 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q8PXB3
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Na/Acetate, Na/Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 27, 2012
RadiationMonochromator: Rotated-inclined double-crystal monochromator, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 57020 / % possible obs: 98.1 % / Redundancy: 4.8 % / Rsym value: 0.089

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WNB

3wnb


Resolution: 1.55→27.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.19 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 5781 10.2 %RANDOM
Rwork0.1735 ---
obs0.1772 51110 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.64 Å2 / Biso mean: 24.0502 Å2 / Biso min: 6.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 26 307 3098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192885
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.9813907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54924.957115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93615536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8771515
X-RAY DIFFRACTIONr_chiral_restr0.2330.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212121
X-RAY DIFFRACTIONr_rigid_bond_restr9.40932885
X-RAY DIFFRACTIONr_sphericity_free25.581565
X-RAY DIFFRACTIONr_sphericity_bonded18.94353083
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 399 -
Rwork0.178 3540 -
all-3939 -
obs--99.9 %

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