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- PDB-2yyo: Crystal structure of human SPRY domain -

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Basic information

Entry
Database: PDB / ID: 2yyo
TitleCrystal structure of human SPRY domain
ComponentsSPRY domain-containing protein 3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SPRY domain / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


SPRY domain-containing protein 3, SPRY domain / : / 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 / Concanavalin A-like lectin/glucanase domain superfamily ...SPRY domain-containing protein 3, SPRY domain / : / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
SPRY domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKishishita, S. / Uchikubo-Kamo, T. / Murayama, K. / Terada, T. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Shirouzu, M. / Wang, B.C. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of human SPRY domain
Authors: Kishishita, S. / Uchikubo-Kamo, T. / Murayama, K. / Terada, T. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Shirouzu, M. / Wang, B.C. / Yokoyama, S.
History
DepositionApr 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: citation / struct ...citation / struct / struct_conn / struct_ref_seq_dif
Item: _citation.title / _struct.title ..._citation.title / _struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPRY domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)18,2621
Polymers18,2621
Non-polymers00
Water1,63991
1
A: SPRY domain-containing protein 3

A: SPRY domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)36,5242
Polymers36,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.107, 52.107, 108.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

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Components

#1: Protein SPRY domain-containing protein 3


Mass: 18261.812 Da / Num. of mol.: 1 / Fragment: SPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPRYD3 / Plasmid: PK050905-07 / Production host: Cell-free protein synthesis / References: UniProt: Q8NCJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.02 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 1.6M Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9789, 0.9793, 0.971
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2006 / Details: mirrors
RadiationMonochromator: Si II / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
30.9711
ReflectionResolution: 2→50 Å / Num. obs: 18943 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 24.5 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.098 / Net I/σ(I): 78.6
Reflection shellResolution: 2→2.11 Å / Mean I/σ(I) obs: 20.4 / Rsym value: 0.348 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→26.05 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 213101.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 943 5 %RANDOM
Rwork0.218 ---
obs0.218 18943 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1519 Å2 / ksol: 0.339151 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2--3.24 Å20 Å2
3----6.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→26.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 0 91 1305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 144 4.6 %
Rwork0.225 2982 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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