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- PDB-3e21: Crystal structure of FAF-1 UBA Domain -

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Basic information

Entry
Database: PDB / ID: 3.0E+21
TitleCrystal structure of FAF-1 UBA Domain
ComponentsFAS-associated factor 1
KeywordsAPOPTOSIS / UBA / Alternative splicing / Nucleus / Phosphoprotein
Function / homology
Function and homology information


ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / : ...ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / : / heat shock protein binding / positive regulation of DNA replication / ubiquitin binding / positive regulation of protein-containing complex assembly / positive regulation of protein catabolic process / nuclear envelope / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of apoptotic process / protein domain specific binding / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. ...: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPark, J.K. / Kim, E.E.
CitationJournal: To be Published
Title: Crystal structure of FAF-1 UBA Domain
Authors: Park, J.K. / Kim, E.E.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)4,9351
Polymers4,9351
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.515, 34.757, 36.129
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/peptide FAS-associated factor 1 / hFAF1


Mass: 4934.514 Da / Num. of mol.: 1 / Fragment: Ubiquitin-associated Domain, UNP residues 5-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNN5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.2M ammonium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2007 / Details: mirrors
RadiationMonochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→19.61 Å / Num. obs: 4463 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.73→1.79 Å / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 6.72 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DAM

2dam


Resolution: 1.73→19.61 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 233801.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 235 5.4 %RANDOM
Rwork0.218 ---
obs0.218 4359 98.2 %-
all-4463 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4121 Å2 / ksol: 0.379249 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2--1.35 Å20 Å2
3---0.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.73→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms309 0 0 32 341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.071.5
X-RAY DIFFRACTIONc_mcangle_it5.152
X-RAY DIFFRACTIONc_scbond_it3.982
X-RAY DIFFRACTIONc_scangle_it6.162.5
LS refinement shellResolution: 1.73→1.84 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 43 6.2 %
Rwork0.235 648 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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