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- PDB-1y02: Crystal Structure of a FYVE-type domain from caspase regulator CARP2 -

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Basic information

Entry
Database: PDB / ID: 1y02
TitleCrystal Structure of a FYVE-type domain from caspase regulator CARP2
ComponentsFYVE-RING finger protein SAKURA
KeywordsMETAL BINDING PROTEIN / CARP2 / FYVE / zinc-binding module / phosphoinositide binding / caspase regulation
Function / homology
Function and homology information


negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / regulation of fibroblast migration / regulation of TOR signaling / negative regulation of signal transduction by p53 class mediator / protein K48-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of signal transduction by p53 class mediator / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity ...negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / regulation of fibroblast migration / regulation of TOR signaling / negative regulation of signal transduction by p53 class mediator / protein K48-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of signal transduction by p53 class mediator / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / recycling endosome membrane / Regulation of TP53 Degradation / p53 binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protease binding / endosome membrane / ubiquitin protein ligase binding / apoptotic process / protein kinase binding / membrane / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #140 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase rififylin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsTibbetts, M.D. / Gu, L. / Shiozaki, E.N. / Shi, Y.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2.
Authors: Tibbetts, M.D. / Shiozaki, E.N. / Gu, L. / McDonald, E.R. / El-Deiry, W.S. / Shi, Y.
History
DepositionNov 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FYVE-RING finger protein SAKURA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7253
Polymers13,5941
Non-polymers1312
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.196, 51.196, 38.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein FYVE-RING finger protein SAKURA / CARP2


Mass: 13593.707 Da / Num. of mol.: 1 / Fragment: CARP2 fragment (residues 26-145)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WZ73
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, Na, K, Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2004
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.7→99 Å / Num. all: 12581 / Num. obs: 12241 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.071
Reflection shellResolution: 1.7→1.76 Å / Rsym value: 0.446 / % possible all: 85.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2338 519 random
Rwork0.206 --
all0.21 10491 -
obs0.21 10239 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 2 153 879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.37

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