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

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Basic information

Entry
Database: PDB / ID: 4kfv
TitleStructural insight into Golgi membrane stacking by GRASP65 and GRASP55
ComponentsGolgi reassembly-stacking protein 1
KeywordsSIGNALING PROTEIN / PDZ Domain / Golgi stacking protein / Golgi
Function / homology
Function and homology information


COPI-mediated anterograde transport / establishment of protein localization to plasma membrane / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of dendrite morphogenesis / COPII-mediated vesicle transport / protein N-linked glycosylation / Golgi organization / protein transport / Golgi membrane / Golgi apparatus ...COPI-mediated anterograde transport / establishment of protein localization to plasma membrane / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of dendrite morphogenesis / COPII-mediated vesicle transport / protein N-linked glycosylation / Golgi organization / protein transport / Golgi membrane / Golgi apparatus / membrane / 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 / Golgi reassembly-stacking protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _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: Golgi reassembly-stacking protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1523
Polymers23,0511
Non-polymers1012
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.989, 104.287, 37.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Golgi reassembly-stacking protein 1 / Gorasp1 protein / RCG25352 / isoform CRA_b


Mass: 23050.912 Da / Num. of mol.: 1 / Fragment: UNP residues 12-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gorasp1, GRASP 65, rCG_25352 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1WBR1, UniProt: O35254*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 5.5
Details: 0.1 M Bis-Tris (pH 5.5) 25% PEG3350, LIQUID DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 60785 / Num. obs: 9540 / % possible obs: 99.3 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.42196.5
2.42-2.991100
2.94-3.76199.3
3.76-4.74199
4.74-5.971100
5.97-40198.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.063 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 453 4.77 %RANDOM
Rwork0.2139 ---
obs0.2171 9497 99.09 %-
all-9540 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.99 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6059 Å20 Å20 Å2
2--0.4458 Å20 Å2
3---2.1601 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 2 97 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081587
X-RAY DIFFRACTIONf_angle_d1.1492150
X-RAY DIFFRACTIONf_dihedral_angle_d17.372582
X-RAY DIFFRACTIONf_chiral_restr0.084229
X-RAY DIFFRACTIONf_plane_restr0.005283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.51780.34011480.2404291398
2.5178-3.17180.31171620.22522992100
3.1718-34.0670.24831430.2019313999

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