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- PDB-2i2o: Crystal Structure of an eIF4G-like Protein from Danio rerio -

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Basic information

Entry
Database: PDB / ID: 2i2o
TitleCrystal Structure of an eIF4G-like Protein from Danio rerio
ComponentseIF4G-like protein
KeywordsStructural genomics / unknown function / eIF4G-like protein / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / cap-dependent translational initiation / translation activator activity / regulation of translational initiation / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / MIF4G domain-containing protein B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2010
Title: Crystal structure of an eIF4G-like protein from Danio rerio.
Authors: Bae, E. / Bitto, E. / Bingman, C.A. / McCoy, J.G. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionAug 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eIF4G-like protein
B: eIF4G-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4244
Polymers52,3062
Non-polymers1172
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-23 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)317.796, 40.948, 40.917
Angle α, β, γ (deg.)90.000, 90.260, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 9 - 217 / Label seq-ID: 11 - 219

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein eIF4G-like protein


Mass: 26153.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Dr.38751 (BC090306) / Plasmid: PVP 33K / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q5EAQ1
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.7 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (7% PEG 4K, 0.40 M ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (7% PEG 4K, 0.40 M sodium chloride, 0.1 M MES/Acetate pH 5.5) CRYOPROTECTED WITH 10% PEG 4K, 0.1 M MES/Acetate pH 5.5, 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97925 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2006
Details: HORIZONTAL SAGITALLY FOCUSING SECOND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.92→40.612 Å / Num. obs: 39789 / % possible obs: 97.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.074 / Χ2: 1.458 / Net I/σ(I): 13.377
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.92-1.995.40.2455.76938951.23395.5
1.99-2.076.30.22239151.23497
2.07-2.166.50.16739311.22296.9
2.16-2.286.40.13639431.18997
2.28-2.426.50.11739041.29696.4
2.42-2.616.50.10538811.41396.6
2.61-2.876.40.08939751.43897.3
2.87-3.286.50.06939921.71198.1
3.28-4.146.50.05741331.59599.6
4.14-40.617.10.05442202.062100

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.92 Å / Lowest resolution: 39.72 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100371242624
ANO_10.6441.739364680
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_18.4-39.7200392136
ISO_16.01-8.400755141
ISO_14.92-6.0100993145
ISO_14.27-4.92001167133
ISO_13.83-4.27001317136
ISO_13.5-3.83001488139
ISO_13.24-3.5001600132
ISO_13.03-3.24001735131
ISO_12.86-3.03001800124
ISO_12.71-2.86001930120
ISO_12.59-2.71002015118
ISO_12.48-2.59002132134
ISO_12.38-2.48002168128
ISO_12.29-2.38002264121
ISO_12.22-2.29002402130
ISO_12.15-2.22002403129
ISO_12.08-2.15002531127
ISO_12.02-2.08002615136
ISO_11.97-2.02002704129
ISO_11.92-1.97002713135
ANO_18.4-39.720.4942.4253920
ANO_16.01-8.40.3473.7977550
ANO_14.92-6.010.4113.2279930
ANO_14.27-4.920.5312.40811660
ANO_13.83-4.270.5692.22413110
ANO_13.5-3.830.5362.22714660
ANO_13.24-3.50.5432.24415700
ANO_13.03-3.240.5482.30816940
ANO_12.86-3.030.5332.33717580
ANO_12.71-2.860.5972.06518810
ANO_12.59-2.710.5981.93419650
ANO_12.48-2.590.6321.72220940
ANO_12.38-2.480.6611.59821420
ANO_12.29-2.380.711.45622370
ANO_12.22-2.290.7711.23223630
ANO_12.15-2.220.7861.20523690
ANO_12.08-2.150.8031.0825070
ANO_12.02-2.080.8440.9625900
ANO_11.97-2.020.8520.86226470
ANO_11.92-1.970.8960.73925680
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1103.773-18.09918.977SE24.281.19
242.959-23.54917.219SE201.16
3121.96715.6111.601SE19.371.07
4133.903-20.75616.55SE26.221.01
553.422-6.20717.148SE35.011.01
626.294-515.713SE32.810.92
7125.34214.37812.89SE14.210.68
846.3696.02415.967SE18.390.64
949.154-1.53515.586SE15.970.55
10128.01113.93420.482SE13.120.35
1143.995.39118.714SE14.720.44
12122.906-23.91113.509SE11.60.37
13128.8598.43615.017SE19.610.33
1449.873.95410.12SE17.850.24
15128.9399.0918.781SE22.420.13
1659.389-25.6748.552SE22.420.06
17108.9920.0929.395SE27.20.22
1848.6721.44510.151SE20.20.11
19112.3062.56321.624SE20.20.1
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 39747
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.58-10066.30.764507
6.62-8.5862.60.898567
5.59-6.6256.60.894699
4.92-5.5957.50.926794
4.45-4.9253.50.935844
4.09-4.4559.40.939935
3.81-4.0956.40.9341042
3.58-3.8157.80.921116
3.38-3.5859.70.9281122
3.22-3.3857.50.9151225
3.07-3.2259.50.9291257
2.95-3.0757.40.9131277
2.84-2.9557.70.921390
2.74-2.8457.90.9161348
2.65-2.7458.70.9171480
2.56-2.6559.40.9161457
2.49-2.56580.9151553
2.42-2.4959.60.9111510
2.36-2.4260.30.9151659
2.3-2.3659.90.9121609
2.25-2.363.30.9021697
2.2-2.2561.70.9121739
2.15-2.264.70.911742
2.1-2.1563.50.9021849
2.06-2.168.10.8931799
2.02-2.0669.20.8751883
1.99-2.02690.8691920
1.92-1.9973.20.8053727

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Processing

Software
NameVersionClassificationNB
HKLdata processing
SHARPphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKLdata scaling
PHENIX(HYSS)phasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.92→40.612 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.207 / SU B: 6.887 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1998 5.024 %RANDOM
Rwork0.19 ---
all0.192 ---
obs0.192 39773 97.423 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.771 Å20 Å2-0.37 Å2
2---0.237 Å20 Å2
3----0.537 Å2
Refinement stepCycle: LAST / Resolution: 1.92→40.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 2 418 3857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223533
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9734763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12424.696181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16215687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6821526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022636
X-RAY DIFFRACTIONr_nbd_refined0.2090.21838
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2334
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.222
X-RAY DIFFRACTIONr_mcbond_it0.711.52190
X-RAY DIFFRACTIONr_mcangle_it1.123420
X-RAY DIFFRACTIONr_scbond_it2.00131513
X-RAY DIFFRACTIONr_scangle_it2.9914.51341
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1715 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.270.5
MEDIUM THERMAL0.522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.9690.2771200.2312729298995.316
1.969-2.0230.2551400.2042705292797.198
2.023-2.0820.2571360.2072619284596.837
2.082-2.1460.2791240.1922543277896.004
2.146-2.2160.2251230.192416260897.354
2.216-2.2940.281370.1872401262396.759
2.294-2.3810.2531260.1932263248096.331
2.381-2.4780.251080.1952195238596.562
2.478-2.5880.2531220.1992152235196.725
2.588-2.7140.2361030.2082035221396.611
2.714-2.8610.241160.1931943210897.676
2.861-3.0350.2621020.1871817197297.312
3.035-3.2440.225960.1931772189698.523
3.244-3.5040.194670.1761666174699.255
3.504-3.8380.255820.1731529161599.752
3.838-4.2910.216890.16913741463100
4.291-4.9540.197820.16412281310100
4.954-6.0660.241470.19810761123100
6.066-8.5720.25430.221838881100
8.572-40.6120.158350.19947451299.414

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