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

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Basic information

Entry
Database: PDB / ID: 2jik
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 / regulation of endocytosis / protein targeting / Rho protein signal transduction / 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: 1.35 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ref_seq.db_align_beg
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
B: SYNAPTOJANIN-2 BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,0682
Polymers22,0682
Non-polymers00
Water4,324240
1
A: SYNAPTOJANIN-2 BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,0341
Polymers11,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SYNAPTOJANIN-2 BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,0341
Polymers11,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.482, 38.335, 60.745
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99955, -0.03004, -0.00035), (-0.03001, 0.9988, -0.03862), (0.00151, -0.03859, -0.99925)
Vector: 30.88531, 1.28447, 29.7834)

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Components

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


Mass: 11034.173 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 6-100
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.88 Å3/Da / Density % sol: 34.75 %
Crystal growpH: 4
Details: 20% PEG6K, 1M LITHIUM CHLORIDE, 0.1M CITRATE PH4.0, pH 4.00

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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: 1.35→38.35 Å / Num. obs: 35482 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.3 / % possible all: 97.4

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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: 1.35→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.4 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1788 5 %RANDOM
Rwork0.17 ---
obs0.173 33676 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.46 Å2
2---0.54 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 0 240 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211605
X-RAY DIFFRACTIONr_bond_other_d0.0030.021059
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9622172
X-RAY DIFFRACTIONr_angle_other_deg1.01232605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82824.88486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.06915290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3051514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
X-RAY DIFFRACTIONr_nbd_refined0.1920.2278
X-RAY DIFFRACTIONr_nbd_other0.1940.21090
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2779
X-RAY DIFFRACTIONr_nbtor_other0.0810.2915
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.06131068
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.73551612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0878635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.47311558
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: 1.35→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 142
Rwork0.167 2416

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