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- PDB-4aiw: GAPR-1 with bound inositol hexakisphosphate -

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Basic information

Entry
Database: PDB / ID: 4aiw
TitleGAPR-1 with bound inositol hexakisphosphate
ComponentsGOLGI-ASSOCIATED PLANT PATHOGENESIS-RELATED PROTEIN 1
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / GOLGI APPARATUS / MYRISTATE
Function / homology
Function and homology information


sexual reproduction / 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 / Cysteine-rich secretory protein family / CAP superfamily ...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 / Cysteine-rich secretory protein family / CAP superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Golgi-associated plant pathogenesis-related protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchouten, A. / Gros, P. / Helms, J.B.
Citation
Journal: Biochim.Biophys.Acta / Year: 2012
Title: Interaction of Gapr-1 with Lipid Bilayers is Regulated by Alternative Homodimerization.
Authors: Van Galen, J. / Olrichs, N.K. / Schouten, A. / Serrano, R.L. / Nolte-'T Hoen, E.N.M. / Eerland, R. / Kaloyanova, D. / Gros, P. / Helms, J.B.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Structural Analysis of the Human Golgi-Associated Plant Pathogenesis Related Protein Gapr-1 Implicates Dimerization as a Regulatory Mechanism.
Authors: Serrano, R.L. / Kuhn, A. / Hendricks, A. / Helms, J.B. / Sinning, I. / Groves, M.R.
History
DepositionFeb 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Oct 7, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-ASSOCIATED PLANT PATHOGENESIS-RELATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9522
Polymers17,2921
Non-polymers6601
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.088, 64.872, 103.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GOLGI-ASSOCIATED PLANT PATHOGENESIS-RELATED PROTEIN 1 / GAPR-1 / GOLGI-ASSOCIATED PR-1 PROTEIN / GLIOMA PATHOGENESIS- RELATED PROTEIN 2 / GLIPR 2


Mass: 17292.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL-1 / References: UniProt: Q9H4G4
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 100 MM MMT, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2007 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→22.04 Å / Num. obs: 21759 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SMB

1smb


Resolution: 1.5→36.46 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.438 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18736 1116 5.1 %RANDOM
Rwork0.15247 ---
obs0.15422 20632 90.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 36 173 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221300
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9661778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42524.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61415219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.431156
X-RAY DIFFRACTIONr_chiral_restr0.1330.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021990
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1811.5774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02521245
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1363526
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8814.5525
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 91 -
Rwork0.201 1552 -
obs--93.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6404-0.73390.09171.4889-0.12053.87680.04590.01370.0859-0.0387-0.0122-0.0078-0.2781-0.1632-0.03380.04680.03960.00460.04940.00160.0612-11.32514.8910.877
20.8459-0.0674-0.17160.69-0.18211.1439-0.0064-0.04160.02310.0243-0.0131-0.1453-0.06510.09760.01950.0252-0.0088-0.01160.01710.00450.05275.1328.8997.788
30.56970.3873-0.13822.2118-1.40573.81080.0462-0.0055-0.0221-0.1102-0.02470.090.354-0.2016-0.02150.0603-0.0174-0.01440.0459-0.00860.0465-10.6370.1289.851
40.55350.1234-0.43330.9241-0.28842.11970.0036-0.02440.0040.06750.0050.0629-0.0092-0.1797-0.00850.0268-0.0032-0.01120.0458-0.00410.043-6.4485.97515.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 32
2X-RAY DIFFRACTION2A33 - 72
3X-RAY DIFFRACTION3A73 - 103
4X-RAY DIFFRACTION4A104 - 154

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