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- PDB-3aj4: Crystal structure of the PH domain of Evectin-2 from human comple... -

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Basic information

Entry
Database: PDB / ID: 3aj4
TitleCrystal structure of the PH domain of Evectin-2 from human complexed with O-phospho-L-serine
ComponentsPleckstrin homology domain-containing family B member 2
KeywordsPROTEIN TRANSPORT / antiparallel BETA sheet
Function / homology
Function and homology information


regulation of cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / recycling endosome 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
PHOSPHOSERINE / Pleckstrin homology domain-containing family B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsOkazaki, S. / Kato, R. / Wakatsuki, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Intracellular phosphatidylserine is essential for retrograde membrane traffic through endosomes
Authors: Uchida, Y. / Hasegawa, J. / Chinnapen, D. / Inoue, T. / Okazaki, S. / Kato, R. / Wakatsuki, S. / Misaki, R. / Koike, M. / Uchiyama, Y. / Iemura, S. / Natsume, T. / Kuwahara, R. / Nakagawa, T. ...Authors: Uchida, Y. / Hasegawa, J. / Chinnapen, D. / Inoue, T. / Okazaki, S. / Kato, R. / Wakatsuki, S. / Misaki, R. / Koike, M. / Uchiyama, Y. / Iemura, S. / Natsume, T. / Kuwahara, R. / Nakagawa, T. / Nishikawa, K. / Mukai, K. / Miyoshi, E. / Taniguchi, N. / Sheff, D. / Lencer, W.I. / Taguchi, T. / Arai, H.
History
DepositionMay 21, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Pleckstrin homology domain-containing family B member 2
B: Pleckstrin homology domain-containing family B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5656
Polymers26,1942
Non-polymers3714
Water5,549308
1
A: Pleckstrin homology domain-containing family B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3443
Polymers13,0971
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pleckstrin homology domain-containing family B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2213
Polymers13,0971
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.747, 48.449, 64.323
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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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) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96CS7
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 1.89 Å3/Da / Density % sol: 34.82 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 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→100 Å / Num. obs: 102125 / % possible obs: 97.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 46.8
Reflection shellResolution: 1→1.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 8.5 / % possible all: 95.3

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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
Starting model: PDB ENTRY 2DHI

2dhi


Resolution: 1→14.45 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.431 / SU ML: 0.011 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12563 5104 5 %RANDOM
Rwork0.10505 ---
obs0.10606 96954 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1→14.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 23 308 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212162
X-RAY DIFFRACTIONr_bond_other_d0.0010.021517
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9412941
X-RAY DIFFRACTIONr_angle_other_deg1.01233703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.095276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64224.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12715.036414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8971515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022495
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02438
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_it1.7991.51295
X-RAY DIFFRACTIONr_mcbond_other0.5391.5515
X-RAY DIFFRACTIONr_mcangle_it2.7722125
X-RAY DIFFRACTIONr_scbond_it3.9373867
X-RAY DIFFRACTIONr_scangle_it5.5494.5816
X-RAY DIFFRACTIONr_rigid_bond_restr1.48633679
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 374 -
Rwork0.131 6840 -
obs--94.36 %

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