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- PDB-2jin: Crystal structure of PDZ domain of Synaptojanin-2 binding protein -

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Basic information

Entry
Database: PDB / ID: 2jin
TitleCrystal structure of PDZ domain of Synaptojanin-2 binding protein
ComponentsSYNAPTOJANIN-2 BINDING PROTEIN
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE / OUTER MEMBRANE / MITOCHONDRIA DISTRIBUTION / PDZ / MEMBRANE / SCAFFOLD / MITOCHONDRION
Function / homology
Function and homology information


negative regulation of sprouting angiogenesis / regulation of Notch signaling pathway / negative regulation of endothelial cell migration / negative regulation of endothelial cell proliferation / negative regulation of angiogenesis / negative regulation of ERK1 and ERK2 cascade / mitochondrial outer membrane / mitochondrion
Similarity search - Function
: / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Synaptojanin-2-binding protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTickle, J. / Phillips, C. / Pike, A.C.W. / Cooper, C. / Salah, E. / Elkins, J. / Turnbull, A.P. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Tickle, J. / Phillips, C. / Pike, A.C.W. / Cooper, C. / Salah, E. / Elkins, J. / Turnbull, A.P. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.
CitationJournal: To be Published
Title: Crystal Structure of Pdz Domain of Synaptojanin-2 Binding Protein
Authors: Tickle, J. / Phillips, C. / Pike, A.C.W. / Cooper, C. / Salah, E. / Elkins, J. / Turnbull, A.P. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Doyle, D.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNAPTOJANIN-2 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2963
Polymers11,1771
Non-polymers1192
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.993, 65.993, 41.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein SYNAPTOJANIN-2 BINDING PROTEIN / MITOCHONDRIAL OUTER MEMBRANE PROTEIN 25


Mass: 11177.340 Da / Num. of mol.: 1 / Fragment: PDZ DOMAIN, RESIDUES 4-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P57105
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT INCLUDES A CARBOXY-TERMINAL TETRAPEPTIDE (ESSI) CORRESPONDING TO A MODE1 PDZ INTERACTION MOTIF

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growpH: 4.5
Details: 30% PEG10K, 0.20M LITHIUM SULPHATE, 0.1M ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 1.5→46.68 Å / Num. obs: 14288 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 14.38 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FE5

2fe5


Resolution: 1.5→46.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.107 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 716 5 %RANDOM
Rwork0.166 ---
obs0.169 13546 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 6 119 905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021856
X-RAY DIFFRACTIONr_bond_other_d0.0020.02567
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.961160
X-RAY DIFFRACTIONr_angle_other_deg2.02931394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90425.41748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.291157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02972
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02163
X-RAY DIFFRACTIONr_nbd_refined0.2490.2156
X-RAY DIFFRACTIONr_nbd_other0.2140.2620
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2417
X-RAY DIFFRACTIONr_nbtor_other0.0950.2477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4243525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6055852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.88335
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.1211307
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 44
Rwork0.235 928
Refinement TLS params.Method: refined / Origin x: -18.62 Å / Origin y: -8.416 Å / Origin z: -22.463 Å
111213212223313233
T-0.112 Å20.0039 Å20.0007 Å2--0.1135 Å2-0.0009 Å2---0.1053 Å2
L0.9174 °2-0.408 °20.3298 °2-1.1031 °2-0.1665 °2--1.3272 °2
S-0.0611 Å °-0.0323 Å °0.0724 Å °-0.009 Å °0.0396 Å °-0.0195 Å °-0.021 Å °0.0289 Å °0.0215 Å °

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