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- PDB-5fms: mmIFT52 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5fms
TitlemmIFT52 N-terminal domain
ComponentsINTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG
KeywordsTRANSPORT PROTEIN / INTRAFLAGELLAR TRANSPORT / IFTB / IFT52 / PROTEIN-PROTEIN INTERACTION
Function / homology
Function and homology information


dendrite terminus / photoreceptor cell cilium / intraciliary anterograde transport / intraciliary transport particle B / Intraflagellar transport / neural tube formation / intraciliary transport / photoreceptor connecting cilium / ciliary tip / Hedgehog 'off' state ...dendrite terminus / photoreceptor cell cilium / intraciliary anterograde transport / intraciliary transport particle B / Intraflagellar transport / neural tube formation / intraciliary transport / photoreceptor connecting cilium / ciliary tip / Hedgehog 'off' state / non-motile cilium assembly / dorsal/ventral pattern formation / regulation of protein processing / determination of left/right symmetry / ciliary base / smoothened signaling pathway / embryonic digit morphogenesis / heart looping / cilium assembly / centriole / ciliary basal body / cilium / negative regulation of epithelial cell proliferation / centrosome
Similarity search - Function
ABC-type uncharacterised transport system / ABC-type uncharacterized transport system / Intraflagellar transport protein 52 homolog
Similarity search - Domain/homology
Intraflagellar transport protein 52 homolog
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.488 Å
AuthorsMourao, A. / Lorentzen, E.
CitationJournal: Embo J. / Year: 2016
Title: Intraflagellar Transport Proteins 172, 80, 57, 54, 38, and 20 Form a Stable Tubulin-Binding Ift-B2 Complex.
Authors: Taschner, M. / Weber, K. / Mourao, A. / Vetter, M. / Awasthi, M. / Stiegler, M. / Bhogaraju, S. / Lorentzen, E.
History
DepositionNov 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG
B: INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG
C: INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)90,8773
Polymers90,8773
Non-polymers00
Water00
1
A: INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,2921
Polymers30,2921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,2921
Polymers30,2921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)30,2921
Polymers30,2921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.910, 204.910, 204.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein INTRAFLAGELLAR TRANSPORT PROTEIN 52 HOMOLOG / PROTEIN NGD5 / IFT52


Mass: 30292.393 Da / Num. of mol.: 3 / Fragment: GIFT, RESIDUES 1-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PEC-A-HT-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62559

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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: 3.96 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 100 MM BIS-TRIS PH5.5, 1.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.49→48.3 Å / Num. obs: 35358 / % possible obs: 99.6 % / Observed criterion σ(I): 1.66 / Redundancy: 21 % / Biso Wilson estimate: 104.38 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 11.29
Reflection shellResolution: 3.49→3.61 Å / Redundancy: 20.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.65 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FMR

5fmr


Resolution: 3.488→48.298 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1755 5 %
Rwork0.2288 --
obs0.2317 35301 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.1 Å2
Refinement stepCycle: LAST / Resolution: 3.488→48.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 0 0 4681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184777
X-RAY DIFFRACTIONf_angle_d1.6026527
X-RAY DIFFRACTIONf_dihedral_angle_d14.8411519
X-RAY DIFFRACTIONf_chiral_restr0.079783
X-RAY DIFFRACTIONf_plane_restr0.007829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4881-3.58240.41371320.33692521X-RAY DIFFRACTION96
3.5824-3.68780.39541340.32392556X-RAY DIFFRACTION100
3.6878-3.80680.33361360.28672597X-RAY DIFFRACTION100
3.8068-3.94280.34171350.26932578X-RAY DIFFRACTION100
3.9428-4.10050.30161370.25162609X-RAY DIFFRACTION100
4.1005-4.28710.2751360.23152582X-RAY DIFFRACTION100
4.2871-4.51290.24631300.19662561X-RAY DIFFRACTION100
4.5129-4.79540.20571420.19232611X-RAY DIFFRACTION100
4.7954-5.16530.22471320.19622581X-RAY DIFFRACTION100
5.1653-5.68440.27871390.22062589X-RAY DIFFRACTION100
5.6844-6.50520.30411390.24072566X-RAY DIFFRACTION100
6.5052-8.18940.25761340.24672598X-RAY DIFFRACTION100
8.1894-48.30240.33721290.19292597X-RAY DIFFRACTION99

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