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- PDB-1nz6: Crystal Structure of Auxilin J-Domain -

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Basic information

Entry
Database: PDB / ID: 1nz6
TitleCrystal Structure of Auxilin J-Domain
ComponentsAuxilin
KeywordsPROTEIN BINDING / Alpha Helix / Anti-Parallel Helix Hairpin
Function / homology
Function and homology information


regulation of clathrin coat assembly / synaptic vesicle recycling / synaptic vesicle uncoating / clathrin heavy chain binding / clathrin coat disassembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / clathrin-dependent endocytosis / clathrin-coated vesicle / clathrin binding / intracellular transport ...regulation of clathrin coat assembly / synaptic vesicle recycling / synaptic vesicle uncoating / clathrin heavy chain binding / clathrin coat disassembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / clathrin-dependent endocytosis / clathrin-coated vesicle / clathrin binding / intracellular transport / dephosphorylation / heat shock protein binding / protein tyrosine phosphatase activity / SH3 domain binding / presynapse / vesicle / postsynaptic density / molecular adaptor activity / protein domain specific binding / intracellular membrane-bounded organelle / cytoplasm
Similarity search - Function
Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJiang, J. / Taylor, A.B. / Prasad, K. / Ishikawa-Brush, Y. / Hart, P.J. / Lafer, E.M. / Sousa, R.
CitationJournal: Biochemistry / Year: 2003
Title: Structure-function analysis of the auxilin J-domain reveals an extended Hsc70 interaction interface.
Authors: Jiang, J. / Taylor, A.B. / Prasad, K. / Ishikawa-Brush, Y. / Hart, P.J. / Lafer, E.M. / Sousa, R.
History
DepositionFeb 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxilin
B: Auxilin


Theoretical massNumber of molelcules
Total (without water)24,0492
Polymers24,0492
Non-polymers00
Water37821
1
A: Auxilin


Theoretical massNumber of molelcules
Total (without water)12,0241
Polymers12,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Auxilin


Theoretical massNumber of molelcules
Total (without water)12,0241
Polymers12,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.066, 103.138, 75.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

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Components

#1: Protein Auxilin /


Mass: 12024.309 Da / Num. of mol.: 2 / Fragment: J-Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: brain / Plasmid: pGEX4T-2Aux813-910 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27974
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 4 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 8
Details: PEG 8000, Tris-Cl, TCEP, Glycerol, pH 8.0, microbatch under oil, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-20 mg/mlprotein11
210 mMTris11pH8.0
33 mMTCEP11
415 %glycerol11
512.5 %PEG800011

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9788, 0.9790, 0.9813
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 2002 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.9791
30.98131
ReflectionResolution: 2.5→50 Å / Num. all: 13067 / Num. obs: 12866 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Net I/σ(I): 38.9
Reflection shellHighest resolution: 2.5 Å
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1330 -RANDOM
Rwork0.234 ---
obs0.234 12866 98.5 %-
all-13067 --
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 0 21 1637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.09
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.827
LS refinement shellResolution: 2.5→2.59 Å /
Rfactor% reflection
Rfree0.361 -
Rwork0.334 -
obs-95.2 %
Refinement
*PLUS
Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.827

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