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- PDB-3via: Crystal structure of the PH domain of Evectin-2 from human -

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Basic information

Entry
Database: PDB / ID: 3via
TitleCrystal structure of the PH domain of Evectin-2 from human
ComponentsPleckstrin homology domain-containing family B member 2
KeywordsPROTEIN TRANSPORT / antiparallel BETA sheet
Function / homology
Function and homology information


phosphatidylinositol-3,4,5-trisphosphate binding / regulation of cell differentiation / recycling endosome membrane / membrane
Similarity search - Function
Pleckstrin homology domain-containing family B member 1/2 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Pleckstrin homology domain-containing family B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOkazaki, S. / Kato, R. / Wakatsuki, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2
Authors: Okazaki, S. / Kato, R. / Uchida, Y. / Taguchi, T. / Arai, H. / Wakatsuki, S.
History
DepositionSep 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Mar 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: Pleckstrin homology domain-containing family B member 2
B: Pleckstrin homology domain-containing family B member 2


Theoretical massNumber of molelcules
Total (without water)26,1942
Polymers26,1942
Non-polymers00
Water2,414134
1
A: Pleckstrin homology domain-containing family B member 2


Theoretical massNumber of molelcules
Total (without water)13,0971
Polymers13,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pleckstrin homology domain-containing family B member 2


Theoretical massNumber of molelcules
Total (without water)13,0971
Polymers13,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.283, 54.267, 111.638
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 Pleckstrin homology domain-containing family B member 2 / PH domain-containing family B member 2 / Evectin-2


Mass: 13096.894 Da / Num. of mol.: 2 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHB2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96CS7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG MME 5000, 0.1M bis-tris-HCl, 13% ethylene glycol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. all: 40506 / Num. obs: 21746 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 48
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 8.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→32.77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.891 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25905 1111 5.1 %RANDOM
Rwork0.21975 ---
obs0.22177 20575 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.321 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 134 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9332643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2324.74799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13615364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6761514
X-RAY DIFFRACTIONr_chiral_restr0.080.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021504
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5621.51168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08121903
X-RAY DIFFRACTIONr_scbond_it1.4143780
X-RAY DIFFRACTIONr_scangle_it2.2654.5740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 74 -
Rwork0.248 1481 -
obs--99.04 %

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