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- PDB-1yzm: Structure of Rabenosyn (458-503), Rab4 binding domain -

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Basic information

Entry
Database: PDB / ID: 1yzm
TitleStructure of Rabenosyn (458-503), Rab4 binding domain
ComponentsFYVE-finger-containing Rab5 effector protein rabenosyn-5
KeywordsPROTEIN TRANSPORT / Rab Effector / Rabenosyn / Rab GTPase / vesicular trafficking
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / regulation of Golgi organization / Golgi to lysosome transport / early endosome to Golgi transport / phosphatidylinositol-3-phosphate binding / endosomal transport / small GTPase binding / protein transport / Factors involved in megakaryocyte development and platelet production / early endosome membrane ...Toll Like Receptor 9 (TLR9) Cascade / regulation of Golgi organization / Golgi to lysosome transport / early endosome to Golgi transport / phosphatidylinositol-3-phosphate binding / endosomal transport / small GTPase binding / protein transport / Factors involved in megakaryocyte development and platelet production / early endosome membrane / early endosome / endosome / endosome membrane / intracellular membrane-bounded organelle / extracellular exosome / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Rabenosyn, Rab binding domain / Rabenosyn, Rab binding domain superfamily / : / Rabenosyn Rab binding domain / Rabosyn-5 repeating NPF sequence-motif / Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 ...Rabenosyn, Rab binding domain / Rabenosyn, Rab binding domain superfamily / : / Rabenosyn Rab binding domain / Rabosyn-5 repeating NPF sequence-motif / Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger, FYVE/PHD-type / Few Secondary Structures / Irregular / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
CitationJournal: Nature / Year: 2005
Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FYVE-finger-containing Rab5 effector protein rabenosyn-5


Theoretical massNumber of molelcules
Total (without water)5,9021
Polymers5,9021
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.366, 42.236, 43.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FYVE-finger-containing Rab5 effector protein rabenosyn-5


Mass: 5901.560 Da / Num. of mol.: 1
Fragment: RAB4 binding domain, sequence database residues 458-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: Q9H1K0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.37 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 3, 2003 / Details: osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 7561 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.5
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 531 / Rsym value: 0.221 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine-gp41 (PDB ID; 1AIK.pdb)

1aik


Resolution: 1.5→6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.375 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20537 335 4.5 %RANDOM
Rwork0.19511 ---
all0.208 7679 --
obs0.19556 7104 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.44 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms361 0 0 84 445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021364
X-RAY DIFFRACTIONr_bond_other_d0.0020.02330
X-RAY DIFFRACTIONr_angle_refined_deg0.941.942490
X-RAY DIFFRACTIONr_angle_other_deg0.8023768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.025545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg49.42625.71421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.231566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.785153
X-RAY DIFFRACTIONr_chiral_restr0.0510.255
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0267
X-RAY DIFFRACTIONr_nbd_refined0.2020.280
X-RAY DIFFRACTIONr_nbd_other0.1530.2266
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2169
X-RAY DIFFRACTIONr_nbtor_other0.0750.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.686 23 -
Rwork0.339 434 -
obs--82.79 %

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