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- PDB-5vhg: Crystal structure of pentad mutant GAPR-1 -

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Basic information

Entry
Database: PDB / ID: 5vhg
TitleCrystal structure of pentad mutant GAPR-1
ComponentsGolgi-associated plant pathogenesis-related protein 1
KeywordsPLANT PROTEIN / GAPR-1 / Autophagy / Beclin 1
Function / homology
Function and homology information


positive regulation of epithelial cell migration / positive regulation of epithelial to mesenchymal transition / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / protein homodimerization activity / extracellular space / extracellular exosome
Similarity search - Function
Golgi-associated plant pathogenesis-related protein 1, SCP domain / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family ...Golgi-associated plant pathogenesis-related protein 1, SCP domain / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Golgi-associated plant pathogenesis-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.27 Å
AuthorsLi, Y. / Zhao, Y. / Su, M. / Chakravarthy, S. / Colbert, C.L. / Levine, B. / Sinha, S.C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein.
Authors: Li, Y. / Zhao, Y. / Su, M. / Glover, K. / Chakravarthy, S. / Colbert, C.L. / Levine, B. / Sinha, S.C.
History
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Golgi-associated plant pathogenesis-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7182
Polymers16,6221
Non-polymers961
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.307, 84.665, 51.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Golgi-associated plant pathogenesis-related protein 1 / Golgi-associated PR-1 protein / Glioma pathogenesis-related protein 2 / GliPR 2


Mass: 16621.592 Da / Num. of mol.: 1 / Mutation: H54A, E86A, G102K, H103A, N138G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLIPR2, C9orf19, GAPR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4G4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris pH 5.5, PEG 3350, Li2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.27→25.708 Å / Num. obs: 35987 / % possible obs: 93.8 % / Redundancy: 3.4 % / Net I/σ(I): 11
Reflection shell
Diffraction-ID
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
AUTOMARdata reduction
PHASERphasing
RefinementResolution: 1.27→25.708 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.27
RfactorNum. reflection% reflection
Rfree0.1795 1808 5.02 %
Rwork0.1497 --
obs0.1512 35984 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.39 Å2 / Biso mean: 15.2301 Å2 / Biso min: 5.41 Å2
Refinement stepCycle: final / Resolution: 1.27→25.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 5 230 1406
Biso mean--25.67 28.3 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071245
X-RAY DIFFRACTIONf_angle_d0.8791685
X-RAY DIFFRACTIONf_chiral_restr0.071170
X-RAY DIFFRACTIONf_plane_restr0.005221
X-RAY DIFFRACTIONf_dihedral_angle_d19.636461
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.27-1.30430.28781400.22262580272099
1.3043-1.34270.25911610.203125732734100
1.3427-1.38610.23931440.186626252769100
1.3861-1.43560.22611250.183226062731100
1.4356-1.49310.24561410.176126062747100
1.4931-1.5610.19051220.15232644276699
1.561-1.64330.1981490.14226042753100
1.6433-1.74620.21941410.136926202761100
1.7462-1.8810.16671430.128426402783100
1.881-2.07020.15961190.123926522771100
2.0702-2.36960.15391480.127626622810100
2.3696-2.98480.161330.148626752808100
2.9848-25.71280.15261420.15512689283196

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