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- PDB-2fbe: Crystal Structure of the PRYSPRY-domain -

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Basic information

Entry
Database: PDB / ID: 2fbe
TitleCrystal Structure of the PRYSPRY-domain
ComponentsPREDICTED: similar to ret finger protein-like 1
KeywordsUNKNOWN FUNCTION / dimer / jellyroll beta-sandwich fold
Function / homology
Function and homology information


ubiquitin protein ligase activity / regulation of gene expression / innate immune response / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
RDM domain, Ret finger protein-like / Ret finger protein-like, SPRY/PRY domain / RFPL defining motif (RDM) / zinc finger of C3HC4-type, RING / SPRY domain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain ...RDM domain, Ret finger protein-like / Ret finger protein-like, SPRY/PRY domain / RFPL defining motif (RDM) / zinc finger of C3HC4-type, RING / SPRY domain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ret finger protein-like 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsGruetter, C. / Briand, C. / Capitani, G. / Mittl, P.R. / Gruetter, M.G.
CitationJournal: Febs Lett. / Year: 2006
Title: Structure of the PRYSPRY-domain: Implications for autoinflammatory diseases
Authors: Gruetter, C. / Briand, C. / Capitani, G. / Mittl, P.R. / Papin, S. / Tschopp, J. / Gruetter, M.G.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PREDICTED: similar to ret finger protein-like 1
B: PREDICTED: similar to ret finger protein-like 1
C: PREDICTED: similar to ret finger protein-like 1
D: PREDICTED: similar to ret finger protein-like 1


Theoretical massNumber of molelcules
Total (without water)89,7274
Polymers89,7274
Non-polymers00
Water3,747208
1
A: PREDICTED: similar to ret finger protein-like 1


Theoretical massNumber of molelcules
Total (without water)22,4321
Polymers22,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PREDICTED: similar to ret finger protein-like 1


Theoretical massNumber of molelcules
Total (without water)22,4321
Polymers22,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PREDICTED: similar to ret finger protein-like 1


Theoretical massNumber of molelcules
Total (without water)22,4321
Polymers22,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PREDICTED: similar to ret finger protein-like 1


Theoretical massNumber of molelcules
Total (without water)22,4321
Polymers22,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.220, 77.220, 297.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsPRYSPRY can form a dimer at high concentration and shows a dimer in the crystal structure. The biological assembly could be a monomer or a dimer.

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Components

#1: Protein
PREDICTED: similar to ret finger protein-like 1


Mass: 22431.736 Da / Num. of mol.: 4 / Fragment: PRYSPRY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: gene 19q13.4.1 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 51474829, UniProt: A6NLU0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 2000 MME, 0.55M KSCN, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSLS X06SA10.8999
SYNCHROTRONSLS X06SA20.9786, 0.9793, 0.9001
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDAug 14, 2005
MARMOSAIC 225 mm CCD2CCDAug 14, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.89991
20.97861
30.97931
40.90011
ReflectionResolution: 2.52→40 Å / Num. all: 31707 / Num. obs: 30566 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 52.1 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.1
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3059 / Rsym value: 0.502 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.52→30.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2409019.72 / 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
Rfree0.277 1502 5 %RANDOM
Rwork0.227 ---
obs0.227 30329 96.1 %-
all-31560 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.96 Å2 / ksol: 0.290646 e/Å3
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å20 Å2
2--2.63 Å20 Å2
3----5.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.52→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 0 208 6286
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it2.151.5
X-RAY DIFFRACTIONc_mcangle_it3.532
X-RAY DIFFRACTIONc_scbond_it4.862
X-RAY DIFFRACTIONc_scangle_it6.672.5
LS refinement shellResolution: 2.52→2.68 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 258 5.1 %
Rwork0.324 4842 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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