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- PDB-4qob: Crystal structure of cPOP1 -

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Basic information

Entry
Database: PDB / ID: 4qob
TitleCrystal structure of cPOP1
ComponentsPyrin domain-containing protein 1
KeywordsPROTEIN BINDING / Death domain superfamily
Function / homology
Function and homology information


negative regulation of interleukin-1-mediated signaling pathway / IkappaB kinase complex / protein serine/threonine kinase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / protein serine/threonine kinase binding / positive regulation of interleukin-1 beta production / innate immune response / nucleus / cytosol
Similarity search - Function
Death Domain, Fas / Death Domain, Fas / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pyrin domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPark, H.H.
CitationJournal: To be Published
Title: Crystal structure of cPOP1
Authors: Park, H.H.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Pyrin domain-containing protein 1
B: Pyrin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)22,3862
Polymers22,3862
Non-polymers00
Water39622
1
A: Pyrin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)11,1931
Polymers11,1931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyrin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)11,1931
Polymers11,1931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.458, 94.458, 94.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Pyrin domain-containing protein 1 / PAAD-only protein 1 / Pyrin-only protein 1


Mass: 11193.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYDC1, ASC2, ASCI, POP1, PYC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXC3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.6M sodium formate, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10004
Reflection shellResolution: 2.7→2.78 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0032refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→38.59 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.293 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.695 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29986 778 9.9 %RANDOM
Rwork0.24737 ---
obs0.25244 7061 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.087 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 22 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191404
X-RAY DIFFRACTIONr_bond_other_d0.0010.021458
X-RAY DIFFRACTIONr_angle_refined_deg1.6752.0241886
X-RAY DIFFRACTIONr_angle_other_deg0.84833348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1455172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80223.22662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.21715281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9091516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.773.434694
X-RAY DIFFRACTIONr_mcbond_other2.7463.43693
X-RAY DIFFRACTIONr_mcangle_it4.4345.128864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9164.019708
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.704→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 55 -
Rwork0.36 497 -
obs--96.34 %

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