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- PDB-3i4o: Crystal Structure of Translation Initiation Factor 1 from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 3i4o
TitleCrystal Structure of Translation Initiation Factor 1 from Mycobacterium tuberculosis
ComponentsTranslation initiation factor IF-1
KeywordsTRANSLATION / translation initiation / IF1 / Initiation factor / Protein biosynthesis
Function / homology
Function and homology information


translation initiation factor activity / peptidoglycan-based cell wall / ribosome binding / rRNA binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor IF-1 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Translation initiation factor IF-1 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsHatzopoulos, G.N. / Mueller-Dieckmann, J.
Citation
Journal: Febs Lett. / Year: 2010
Title: Structure of translation initiation factor 1 from Mycobacterium tuberculosis and inferred binding to the 30S ribosomal subunit.
Authors: Hatzopoulos, G.N. / Mueller-Dieckmann, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of initiation factor 1 from Mycobacterium tuberculosis.
Authors: Hatzopoulos, G.N. / Mueller-Dieckmann, J.
History
DepositionJul 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation factor IF-1
B: Translation initiation factor IF-1


Theoretical massNumber of molelcules
Total (without water)18,2712
Polymers18,2712
Non-polymers00
Water2,936163
1
A: Translation initiation factor IF-1


Theoretical massNumber of molelcules
Total (without water)9,1361
Polymers9,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Translation initiation factor IF-1


Theoretical massNumber of molelcules
Total (without water)9,1361
Polymers9,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.95, 76.54, 28.03
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Translation initiation factor IF-1 / Translation Initiation Factor 1


Mass: 9135.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Gene: infA, MCB1222.32c, MT3568, MTCY13E12.15c, Rv3462c, Rv3462c (infA)
Plasmid: pET151/D/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RP / References: UniProt: P0A5H5, UniProt: P9WKK3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 % / Mosaicity: 0.5 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12-16% (w/v) PEG 8000, 50-200mM KCl and 8-16% (v/v) glycerol, pH 4.5, vapor diffusion, hanging drop, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A10.9749
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9201
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDApr 6, 2006
MAR CCD 165 mm2CCDAug 17, 2006
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97491
20.92011
ReflectionRedundancy: 13.7 % / Av σ(I) over netI: 19.63 / Number: 346683 / Rmerge(I) obs: 0.076 / Χ2: 1.07 / D res high: 1.52 Å / D res low: 30 Å / Num. obs: 25215 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.123097.510.051.02212.8
3.274.129910.0480.99213.9
2.863.2799.310.0591.01914.2
2.62.8699.110.071.0414.3
2.412.698.610.0851.06314.4
2.272.4198.110.0811.05614.4
2.162.2798.310.0871.06414.7
2.062.1698.910.0921.07114.4
1.982.0696.110.1061.10314.7
1.911.9899.910.1231.11614.3
1.861.9195.910.1511.12414.5
1.81.8698.810.181.13113.9
1.751.897.710.2141.11614.1
1.711.7595.410.2511.09913.7
1.671.7199.910.3021.09613.4
1.641.6795.110.3391.05513.5
1.61.6495.610.4281.04413.2
1.571.699.910.4731.0112.9
1.551.5794.410.5250.98913.1
1.521.5592.210.6271.08610.4
ReflectionResolution: 1.47→38.27 Å / Num. all: 27919 / Num. obs: 27447 / % possible obs: 98.2 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 4.5 / Redundancy: 7.2 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.063 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.47-1.56.70.35913171.174197
1.5-1.527.30.28113710.99199.9
1.52-1.557.30.25913381.025197.2
1.55-1.587.40.21213511.033198.7
1.58-1.627.30.1913751.0721100
1.62-1.667.40.17913571.092197.2
1.66-1.77.40.15513661.1071100
1.7-1.747.20.14313851.119199.6
1.74-1.797.50.13213491.126198.7
1.79-1.857.30.12413961.1091100
1.85-1.927.40.11113461.091198.8
1.92-1.997.30.10614121.074199.9
1.99-2.097.40.09813741.054199.4
2.09-2.27.30.09313991.045199.6
2.2-2.337.30.09614101.0391100
2.33-2.517.40.0914031.043199.9
2.51-2.777.30.08914141.04199.9
2.77-3.177.20.07914331.023199.7
3.17-3.996.70.06813981.007195.6
3.99-305.80.05212990.978183.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
BESTdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→26.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.891 / SU B: 1.769 / SU ML: 0.033 / SU R Cruickshank DPI: 0.076 / SU Rfree: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1376 5 %RANDOM
Rwork0.159 ---
obs0.16 27447 98.21 %-
all-27919 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.49 Å2 / Biso mean: 21.39 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.47→26.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 0 163 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221298
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9891780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43722.22263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0081516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211028
X-RAY DIFFRACTIONr_mcbond_it1.9091.5774
X-RAY DIFFRACTIONr_mcangle_it2.90521289
X-RAY DIFFRACTIONr_scbond_it3.7793524
X-RAY DIFFRACTIONr_scangle_it5.9334.5486
X-RAY DIFFRACTIONr_rigid_bond_restr2.08331298
X-RAY DIFFRACTIONr_sphericity_bonded5.62931255
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 97 -
Rwork0.155 1896 -
all-1993 -
obs--98.86 %

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