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- PDB-4kfw: Structural insight into Golgi membrane stacking by GRASP65 and GRASP55 -

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Basic information

Entry
Database: PDB / ID: 4kfw
TitleStructural insight into Golgi membrane stacking by GRASP65 and GRASP55
ComponentsGolgi reassembly stacking protein 2
KeywordsSIGNALING PROTEIN / Golgi stacking protein
Function / homology
Function and homology information


organelle organization / establishment of protein localization to plasma membrane / organelle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi medial cisterna / Golgi organization / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation / Golgi membrane ...organelle organization / establishment of protein localization to plasma membrane / organelle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi medial cisterna / Golgi organization / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus
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 2 / Golgi reassembly-stacking protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiu, X. / Hu, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural insight into Golgi membrane stacking by GRASP65 and GRASP55 proteins
Authors: Feng, Y. / Yu, W. / Li, X. / Lin, S. / Zhou, Y. / Hu, J. / Liu, X.
History
DepositionApr 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi reassembly stacking protein 2
B: Golgi reassembly stacking protein 2


Theoretical massNumber of molelcules
Total (without water)47,0452
Polymers47,0452
Non-polymers00
Water1,63991
1
A: Golgi reassembly stacking protein 2


Theoretical massNumber of molelcules
Total (without water)23,5221
Polymers23,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Golgi reassembly stacking protein 2


Theoretical massNumber of molelcules
Total (without water)23,5221
Polymers23,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.077, 83.077, 145.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Golgi reassembly stacking protein 2


Mass: 23522.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gorasp2, rCG_26651 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68G33, UniProt: Q9R064*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8.5
Details: 0.1M Tris (pH 8.5) 25% PEG3350 0.2 M (NH4)2Ac, LIQUID DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 30, 2012
RadiationMonochromator: 0.9793 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 15821 / Num. obs: 14443 / % possible obs: 98.2 % / Observed criterion σ(F): 1.39 / Observed criterion σ(I): 1.39
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7-3.11100
3.1-4.03199.3
4.03-6.891100
6.89-50198.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.81 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 717 5.01 %random
Rwork0.2024 ---
obs0.2067 14320 98.17 %-
all-14443 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.283 Å2 / ksol: 0.289 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0261 Å20 Å20 Å2
2---0.0261 Å2-0 Å2
3---0.0523 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 0 91 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083303
X-RAY DIFFRACTIONf_angle_d1.1124482
X-RAY DIFFRACTIONf_dihedral_angle_d18.061198
X-RAY DIFFRACTIONf_chiral_restr0.074491
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.90850.3481520.25382675100
2.9085-3.20110.32871310.22712724100
3.2011-3.66410.31811450.2023263297
3.6641-4.61540.27391440.1812269197
4.6154-41.81530.24361450.1777288198
Refinement TLS params.Method: refined / Origin x: -41.0705 Å / Origin y: 16.2534 Å / Origin z: -17.6074 Å
111213212223313233
T0.2593 Å20.0205 Å2-0.0297 Å2-0.3087 Å2-0.0031 Å2--0.2962 Å2
L0.3384 °2-0.2463 °20.4393 °2-0.5553 °2-0.4478 °2--0.7512 °2
S-0.0248 Å °-0.1118 Å °0.0141 Å °0.0451 Å °0.0173 Å °0.0932 Å °0.0035 Å °-0.0822 Å °0 Å °
Refinement TLS groupSelection details: all

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