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- PDB-4e6z: Tic22 from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 4e6z
TitleTic22 from Plasmodium falciparum
ComponentsApicoplast TIC22, putative
KeywordsTRANSPORT PROTEIN / TIC complex / import protein / apicoplast
Function / homology
Function and homology information


apicoplast / chloroplast / protein transport / protein folding
Similarity search - Function
Trna Endonuclease; Chain: A, domain 1 - #100 / Tic22-like / Tic22-like family / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Apicoplast TIC22 protein
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1501 Å
AuthorsGlaser, S. / Higgins, M.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Tic22 is an essential chaperone required for protein import into the apicoplast.
Authors: Glaser, S. / van Dooren, G.G. / Agrawal, S. / Brooks, C.F. / McFadden, G.I. / Striepen, B. / Higgins, M.K.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 5, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apicoplast TIC22, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1322
Polymers34,0401
Non-polymers921
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 66.250, 129.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Apicoplast TIC22, putative


Mass: 34040.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFE1460w / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I3H4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9800, 0.9802, 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.98021
30.95371
ReflectionResolution: 2.15→46.283 Å / Num. all: 15234 / Num. obs: 15234 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1501→46.283 Å / SU ML: 0.3 / σ(F): 0.02 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 774 5.08 %
Rwork0.2166 --
obs0.2178 15234 93.11 %
all-15234 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.07 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.0741 Å2-0 Å20 Å2
2---11.0741 Å2-0 Å2
3---22.1483 Å2
Refinement stepCycle: LAST / Resolution: 2.1501→46.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 6 27 1692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031699
X-RAY DIFFRACTIONf_angle_d0.6342281
X-RAY DIFFRACTIONf_dihedral_angle_d17.686642
X-RAY DIFFRACTIONf_chiral_restr0.046246
X-RAY DIFFRACTIONf_plane_restr0.002284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.28480.35151160.31282114X-RAY DIFFRACTION84
2.2848-2.46120.27121200.25092228X-RAY DIFFRACTION88
2.4612-2.70890.32321500.24732336X-RAY DIFFRACTION94
2.7089-3.10080.24551470.2372481X-RAY DIFFRACTION97
3.1008-3.90640.21541310.19982589X-RAY DIFFRACTION99
3.9064-46.29330.2051100.19072712X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66671.4923-1.00152.63313.33562.00030.3673-0.64342.0174-1.0522-0.75461.4053-1.3789-1.06830.26080.79340.00230.0510.6892-0.40861.2495-1.219440.319710.0514
22.90432.64571.45275.55411.36041.2099-0.0433-0.11120.4172-0.43670.06811.658-0.1002-0.5640.07580.3443-0.0425-0.06730.4232-0.05670.5209-4.34421.49911.4632
31.8115-0.23830.4635.383-0.65861.3441-0.0315-0.787-0.81720.9372-0.27040.29010.6625-1.05710.02860.6489-0.24510.02470.54520.10370.62942.022613.490711.3544
44.7671-0.6291-0.72346.94122.19034.0418-0.23020.0614-1.14630.83880.5785-0.20270.68660.3131-0.30020.236-0.0832-0.00510.263-0.10840.3495.504615.1722-2.9405
55.0979-0.01231.56435.5302-1.21260.7457-0.4550.5025-1.6252-1.49570.26510.81410.3112-0.31930.3070.4978-0.094-0.05190.3869-0.16191.5623-2.42784.1478-3.8644
61.79381.2224-0.92312.1604-0.16261.18720.233-0.25910.2281-0.1092-0.220.2405-0.1466-0.44490.02140.3138-0.0301-0.01260.4291-0.09910.5037-3.528624.66154.5037
72.4760.99950.2630.78220.350.1905-0.786-0.1569-0.65380.2325-0.00090.1730.51621.55390.74361.0832-0.52610.20821.1762-0.08230.625-3.434422.492221.336
80.01960.19170.05686.2613-1.14153.3960.18510.0673-0.83150.1367-0.2319-1.32670.2522-0.0160.13760.3451-0.118-0.09630.37840.02290.586712.617424.73996.4257
95.59181.06476.78227.25810.45678.4192-0.9363-1.6281-1.18041.5371.0371-0.7895-0.3309-0.0065-0.54460.5846-0.0459-0.2540.66340.27830.62220.142227.137312.7766
105.84012.6375-2.70454.2022-1.81362.6663-0.13380.07330.9775-0.27480.1790.0376-0.7003-0.143-0.06940.5763-0.147-0.09270.29650.00830.565716.317144.44570.132
110.1684-0.0215-0.12655.7417-4.81354.1478-0.19330.30650.79811.47970.46051.1821-0.9755-0.3325-0.07480.94120.0081-0.08740.5124-0.04010.86978.777739.406714.2849
125.7851-0.3741-0.23281.7376-0.1870.54350.14060.91240.7846-0.28130.0374-0.1942-0.19480.14140.08580.4186-0.1024-0.2030.33710.16260.20350.022629.7102-6.8598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 68:74 )A68 - 74
2X-RAY DIFFRACTION2( CHAIN A AND RESID 75:90 )A75 - 90
3X-RAY DIFFRACTION3( CHAIN A AND RESID 91:103 )A91 - 103
4X-RAY DIFFRACTION4( CHAIN A AND RESID 104:119 )A104 - 119
5X-RAY DIFFRACTION5( CHAIN A AND RESID 120:125 )A120 - 125
6X-RAY DIFFRACTION6( CHAIN A AND RESID 126:141 )A126 - 141
7X-RAY DIFFRACTION7( CHAIN A AND RESID 142:162 )A142 - 162
8X-RAY DIFFRACTION8( CHAIN A AND RESID 163:182 )A163 - 182
9X-RAY DIFFRACTION9( CHAIN A AND RESID 183:193 )A183 - 193
10X-RAY DIFFRACTION10( CHAIN A AND RESID 194:240 )A194 - 240
11X-RAY DIFFRACTION11( CHAIN A AND RESID 241:256 )A241 - 256
12X-RAY DIFFRACTION12( CHAIN A AND RESID 257:275 )A257 - 275

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