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- PDB-1mi1: Crystal Structure of the PH-BEACH Domain of Human Neurobeachin -

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Basic information

Entry
Database: PDB / ID: 1mi1
TitleCrystal Structure of the PH-BEACH Domain of Human Neurobeachin
ComponentsNeurobeachin
KeywordsSIGNALING PROTEIN / PH domain / BEACH domain / vesicle trafficking / signal transduction / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / Assembly and cell surface presentation of NMDA receptors / PKA activation / endomembrane system / trans-Golgi network / NOTCH1 Intracellular Domain Regulates Transcription / protein localization / protein kinase binding / membrane / nucleus ...Neurotransmitter receptors and postsynaptic signal transmission / Assembly and cell surface presentation of NMDA receptors / PKA activation / endomembrane system / trans-Golgi network / NOTCH1 Intracellular Domain Regulates Transcription / protein localization / protein kinase binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Neurobeachin; Chain: A, domain 1 / BEACH domain / Neurobeachin-like, DUF1088 / Neurobeachin/BDCP, DUF4704 / Neurobeachin-like, DUF1088 / Neurobeachin/BDCP, DUF4704 alpha solenoid region / BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain ...Neurobeachin; Chain: A, domain 1 / BEACH domain / Neurobeachin-like, DUF1088 / Neurobeachin/BDCP, DUF4704 / Neurobeachin-like, DUF1088 / Neurobeachin/BDCP, DUF4704 alpha solenoid region / BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain / PH domain associated with Beige/BEACH / BEACH domain profile. / BEACH-type PH domain profile. / Beige/BEACH domain / : / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold / Roll / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsJogl, G. / Shen, Y. / Gebauer, D. / Li, J. / Wiegmann, K. / Kashkar, H. / Kroenke, M. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of the BEACH domain reveals an unusual fold and extensive association with a novel PH domain.
Authors: Jogl, G. / Shen, Y. / Gebauer, D. / Li, J. / Wiegmann, K. / Kashkar, H. / Kronke, M. / Tong, L.
History
DepositionAug 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurobeachin
B: Neurobeachin


Theoretical massNumber of molelcules
Total (without water)96,4342
Polymers96,4342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.910, 179.910, 98.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: Protein Neurobeachin / BCL8B protein / KIAA1544 protein


Mass: 48216.906 Da / Num. of mol.: 2 / Fragment: residues 2150-2563 of GB entry AAM53531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q8NFP9

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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: 4.77 Å3/Da / Density % sol: 74.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Tris, 10mM DTT, 4% PEG 8000, pH 7.6, VAPOR DIFFUSION, SITTING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH7.6
24 %(w/v)PEG80001reservoir
32 mMdithiothreitol1reservoir
420 mMTris1droppH8.5
5200 mM1dropNaCl
610 mMdithiothreitol1drop
730 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9764, 0.9793, 0.9791, 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2001
RadiationMonochromator: mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97641
20.97931
30.97911
40.96861
ReflectionResolution: 2.9→30 Å / Num. all: 39977 / Num. obs: 39977 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 151.6 Å2
Reflection shellResolution: 2.9→3 Å / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 80025 / Num. measured all: 355843 / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
MADSYSphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→29.71 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1995 5 %RANDOM
Rwork0.23 ---
obs0.23 39977 99.1 %-
all-39977 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9675 Å2 / ksol: 0.310806 e/Å3
Displacement parametersBiso mean: 60.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.07 Å213.59 Å20 Å2
2--4.82 Å20 Å2
3----10.89 Å2
Refine analyzeLuzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.61 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 0 0 6654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.468 343 5.2 %
Rwork0.425 6305 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MSE.PARMSE.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Rfactor obs: 0.23 / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.468 / Rfactor Rwork: 0.425

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