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- PDB-3p0c: Nischarin PX-domain -

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Basic information

Entry
Database: PDB / ID: 3p0c
TitleNischarin PX-domain
ComponentsNischarin
KeywordsSIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / PX-domain
Function / homology
Function and homology information


outer dynein arm assembly / dynein heavy chain binding / RND2 GTPase cycle / RND3 GTPase cycle / intercellular bridge / Rac protein signal transduction / alpha-tubulin binding / RAC1 GTPase cycle / negative regulation of cell migration / phosphatidylinositol binding ...outer dynein arm assembly / dynein heavy chain binding / RND2 GTPase cycle / RND3 GTPase cycle / intercellular bridge / Rac protein signal transduction / alpha-tubulin binding / RAC1 GTPase cycle / negative regulation of cell migration / phosphatidylinositol binding / recycling endosome / microtubule cytoskeleton / integrin binding / actin cytoskeleton organization / early endosome / intracellular membrane-bounded organelle / apoptotic process / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nischarin, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat profile. ...Nischarin, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.273 Å
AuthorsSchutz, P. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Schutz, P. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Der Berg, S. / Wahlberg, E. / Welin, M. / Weigelt, J. / Nordlund, P. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of Nischarin PX-domain
Authors: Schutz, P. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kol, S. / ...Authors: Schutz, P. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Der Berg, S. / Wahlberg, E. / Welin, M. / Weigelt, J. / Nordlund, P. / Schuler, H.
History
DepositionSep 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nischarin
B: Nischarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5774
Polymers30,3932
Non-polymers1842
Water2,648147
1
A: Nischarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2882
Polymers15,1961
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nischarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2882
Polymers15,1961
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Nischarin
hetero molecules

B: Nischarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5774
Polymers30,3932
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.880, 64.780, 80.680
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 Nischarin


Mass: 15196.305 Da / Num. of mol.: 2 / Fragment: PX-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NISCH, IRAS, KIAA0975 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q9Y2I1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 11% PEG monomethyl ether 2000, 0.3M NaCl, 0.1M Tris, 0.3M trimetylamine n-oxide, 1mM benzene 1,2,4-trisphosphate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→57.88 Å / Num. obs: 14541 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 21.1
Reflection shellResolution: 2.27→2.4 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 11.4 / Num. unique all: 2071 / Rsym value: 0.215 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.273→50.513 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8721 / SU ML: 0.24 / σ(F): 0.1 / Phase error: 19.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.21 725 5.05 %RANDOM
Rwork0.1737 ---
obs0.1755 14357 98.99 %-
all-14499 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.547 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 101.83 Å2 / Biso mean: 25.8897 Å2 / Biso min: 2.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.6009 Å2-0 Å20 Å2
2---4.2775 Å2-0 Å2
3---0.6766 Å2
Refinement stepCycle: LAST / Resolution: 2.273→50.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 12 147 1914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071811
X-RAY DIFFRACTIONf_angle_d0.9252457
X-RAY DIFFRACTIONf_chiral_restr0.064277
X-RAY DIFFRACTIONf_plane_restr0.004308
X-RAY DIFFRACTIONf_dihedral_angle_d15.025631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.273-2.44850.26791560.18312622277898
2.4485-2.69490.25351410.17972697283899
2.6949-3.08480.20261240.16752712283699
3.0848-3.88630.17641560.158127282884100
3.8863-50.5250.18771480.17372873302199
Refinement TLS params.Method: refined / Origin x: -21.3813 Å / Origin y: -7.8605 Å / Origin z: 8.4111 Å
111213212223313233
T0.0292 Å20.0093 Å20.0029 Å2-0.0399 Å20.0064 Å2--0.015 Å2
L0.4345 °20.1932 °20.0645 °2-0.445 °20.2049 °2--0.1661 °2
S0.0339 Å °-0.0456 Å °-0.0434 Å °-0.0447 Å °-0.0187 Å °-0.093 Å °-0.0319 Å °-0.0475 Å °-0.012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 121
2X-RAY DIFFRACTION1allB16 - 123

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