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- PDB-6g8w: Crystal Structures of the Single PDZ Domains from GRASP65 and the... -

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Basic information

Entry
Database: PDB / ID: 6g8w
TitleCrystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130
ComponentsGolgi reassembly-stacking protein 1
KeywordsPROTEIN BINDING / PDZ2 domain structure / Golgi stacking / GRASP family / Golgins / Golgi apparatus / yeast homolog of GRASP65 / vesicle transport
Function / homology
Function and homology information


establishment of protein localization to plasma membrane / negative regulation of dendrite morphogenesis / Golgi ribbon formation / cis-Golgi network / Golgi Cisternae Pericentriolar Stack Reorganization / protein N-linked glycosylation / COPII-mediated vesicle transport / Golgi organization / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane ...establishment of protein localization to plasma membrane / negative regulation of dendrite morphogenesis / Golgi ribbon formation / cis-Golgi network / Golgi Cisternae Pericentriolar Stack Reorganization / protein N-linked glycosylation / COPII-mediated vesicle transport / Golgi organization / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / protein transport / Golgi membrane / Golgi apparatus / metal ion binding
Similarity search - Function
GRASP55/65 / GRASP-type PDZ domain / GRASP55/65 PDZ-like domain / GRASP-type PDZ domain profile. / PDZ domain / Pdz3 Domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Golgi reassembly-stacking protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsJurk, C.M. / Roske, Y. / Heinemann, U.
CitationJournal: Croatica Chemica Acta / Year: 2018
Title: Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130
Authors: Jurk, C.M. / Roske, Y. / Heinemann, U.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi reassembly-stacking protein 1
B: Golgi reassembly-stacking protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4788
Polymers21,1052
Non-polymers3726
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint13 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.825, 82.613, 49.220
Angle α, β, γ (deg.)90.00, 110.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-342-

HOH

31B-407-

HOH

41B-450-

HOH

51B-451-

HOH

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Components

#1: Protein Golgi reassembly-stacking protein 1 / Golgi peripheral membrane protein p65 / Golgi phosphoprotein 5 / GOLPH5 / Golgi reassembly-stacking ...Golgi peripheral membrane protein p65 / Golgi phosphoprotein 5 / GOLPH5 / Golgi reassembly-stacking protein of 65 kDa / GRASP65


Mass: 10552.704 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GORASP1, GOLPH5, GRASP65 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQQ3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.4M Na/K phosphate pH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.12→26.85 Å / Num. obs: 10762 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rrim(I) all: 0.078 / Net I/σ(I): 15.78
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.97 / Num. unique obs: 788 / CC1/2: 0.999 / Rrim(I) all: 0.626 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLE

3rle


Resolution: 2.12→26.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.298 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23548 538 5 %RANDOM
Rwork0.18597 ---
obs0.18839 10222 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.953 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å2-0 Å2-1.97 Å2
2---1.34 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.12→26.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 24 94 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191433
X-RAY DIFFRACTIONr_bond_other_d0.0020.021282
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.971941
X-RAY DIFFRACTIONr_angle_other_deg1.14332984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6923.89859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.986156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211589
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
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_it3.3553.082716
X-RAY DIFFRACTIONr_mcbond_other3.3563.08715
X-RAY DIFFRACTIONr_mcangle_it5.094.576889
X-RAY DIFFRACTIONr_mcangle_other5.0884.579890
X-RAY DIFFRACTIONr_scbond_it4.0633.562716
X-RAY DIFFRACTIONr_scbond_other4.0613.562716
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2995.1261051
X-RAY DIFFRACTIONr_long_range_B_refined8.95937.2311567
X-RAY DIFFRACTIONr_long_range_B_other8.95737.2491568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 39 -
Rwork0.293 744 -
obs--100 %

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