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- PDB-3kn1: Crystal Structure of Golgi Phosphoprotein 3 N-term Truncation Variant -

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Basic information

Entry
Database: PDB / ID: 3kn1
TitleCrystal Structure of Golgi Phosphoprotein 3 N-term Truncation Variant
ComponentsGolgi phosphoprotein 3
KeywordsPROTEIN BINDING / beta hairpin / phosphoinositide binding domain / Cell membrane / Cytoplasm / Endosome / Golgi apparatus / Membrane / Mitochondrion / Phosphoprotein
Function / homology
Function and homology information


asymmetric Golgi ribbon formation / protein targeting to Golgi apparatus / cargo adaptor activity / Golgi vesicle budding / Golgi cisterna / cellular response to rapamycin / glycoprotein biosynthetic process / protein retention in Golgi apparatus / Golgi ribbon formation / cell adhesion molecule production ...asymmetric Golgi ribbon formation / protein targeting to Golgi apparatus / cargo adaptor activity / Golgi vesicle budding / Golgi cisterna / cellular response to rapamycin / glycoprotein biosynthetic process / protein retention in Golgi apparatus / Golgi ribbon formation / cell adhesion molecule production / leukocyte tethering or rolling / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi to plasma membrane protein transport / phosphatidylinositol-4-phosphate binding / regulation of mitochondrion organization / lamellipodium assembly / Golgi cisterna membrane / Golgi organization / protein secretion / positive regulation of TOR signaling / positive regulation of protein secretion / trans-Golgi network / mitochondrial intermembrane space / cell migration / gene expression / endosome / Golgi membrane / intracellular membrane-bounded organelle / negative regulation of apoptotic process / enzyme binding / Golgi apparatus / mitochondrion / plasma membrane / cytosol
Similarity search - Function
yeast vps74-n-term truncation variant fold / yeast vps74-n-term truncation variant domain like / Golgi phosphoprotein 3-like / Golgi phosphoprotein 3-like domain superfamily / Golgi phosphoprotein 3 (GPP34) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Golgi phosphoprotein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsSchmitz, K.R. / Bessman, N.J. / Setty, T.G. / Ferguson, K.M.
CitationJournal: J.Cell Biol. / Year: 2009
Title: PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to retrograde Golgi trafficking.
Authors: Wood, C.S. / Schmitz, K.R. / Bessman, N.J. / Setty, T.G. / Ferguson, K.M. / Burd, C.G.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Golgi phosphoprotein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3697
Polymers28,7931
Non-polymers5766
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Golgi phosphoprotein 3
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)704,855168
Polymers691,02224
Non-polymers13,833144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area88470 Å2
ΔGint-2145 kcal/mol
Surface area247030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.369, 174.369, 174.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Detailsauthors state that the software-determined 24-mer involves interactions stabilized by non-physiological inter-copy disulfide bonds between symmetry-related copies of chain A.

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Components

#1: Protein Golgi phosphoprotein 3 / Coat protein GPP34 / Mitochondrial DNA absence factor / MIDAS


Mass: 28792.574 Da / Num. of mol.: 1 / Fragment: UNP residues 52-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLPH3, GPP34 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q9H4A6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.9 M (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97951 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10180 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.133 / Χ2: 1.67 / Net I/σ(I): 7.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.4 / Num. unique all: 994 / Χ2: 1.393 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å46.6 Å
Translation2.9 Å46.6 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZIH

2zih


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.816 / SU R Cruickshank DPI: 0.637 / SU Rfree: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.637 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.266 491 4.8 %RANDOM
Rwork0.213 ---
obs0.215 10149 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 109.27 Å2 / Biso mean: 38.227 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 30 9 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221957
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9972659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1935240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7924.53586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.881514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211417
X-RAY DIFFRACTIONr_mcbond_it0.8541.51196
X-RAY DIFFRACTIONr_mcangle_it1.72121926
X-RAY DIFFRACTIONr_scbond_it2.8073761
X-RAY DIFFRACTIONr_scangle_it4.5174.5732
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 39 -
Rwork0.303 682 -
all-721 -
obs--98.63 %

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