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- PDB-5zcy: Crystal structure of archaeal translation initiation factor 1 at ... -

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Basic information

Entry
Database: PDB / ID: 5zcy
TitleCrystal structure of archaeal translation initiation factor 1 at 1.5 Angstroms resolution
ComponentsProtein translation factor SUI1 homolog
KeywordsTRANSLATION / aIF1 / eIF1 / eukaryotic translation initiation / YciH / archaea / eukaryote
Function / homology
Function and homology information


translation initiation factor activity
Similarity search - Function
Translation factor SUI1 homolog, archaea / Archaeal/bacterial translation initiation factor SUI1 / : / SUI1-like domain / Translation Initiation Factor Eif1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRITE ION / NITRATE ION / Protein translation factor SUI1 homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsGogoi, P. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology Government of IndiaBT/302/NE/TBP/2012 India
CitationJournal: FEBS Lett. / Year: 2018
Title: Archaeal and eukaryal translation initiation factor 1 differ in their RNA interacting loops.
Authors: Gogoi, P. / Kanaujia, S.P.
History
DepositionFeb 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: Protein translation factor SUI1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5823
Polymers11,4741
Non-polymers1082
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint1 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.580, 53.580, 56.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein translation factor SUI1 homolog


Mass: 11474.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1771.1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P58193
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2M Lithium Nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 26, 2017 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→35.97 Å / Num. obs: 14801 / % possible obs: 98.1 % / Redundancy: 11 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Net I/σ(I): 23.4
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.514 / Num. unique obs: 691 / CC1/2: 0.915 / Rpim(I) all: 0.165 / Rrim(I) all: 0.54 / % possible all: 95.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.75 Å35.97 Å
Translation3.75 Å35.97 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.2.1data reduction
Aimless0.5.28data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
Coot0.8.6model building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MO0

4mo0


Resolution: 1.5→35.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.083 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0696 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 686 4.6 %RANDOM
Rwork0.1738 ---
obs0.1753 14100 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.26 Å2 / Biso mean: 19.198 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.5→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms671 0 7 82 760
Biso mean--23.17 30.99 -
Num. residues----83
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.019680
X-RAY DIFFRACTIONr_bond_other_d0.0020.02707
X-RAY DIFFRACTIONr_angle_refined_deg2.5782.012900
X-RAY DIFFRACTIONr_angle_other_deg1.09831633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.112582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44924.68832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6115152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.189156
X-RAY DIFFRACTIONr_chiral_restr0.1590.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02740
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02136
LS refinement shellResolution: 1.495→1.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 29 -
Rwork0.318 1033 -
all-1062 -
obs--95.59 %

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