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- PDB-4uml: Crystal structure of ganglioside induced differentiation associat... -

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Basic information

Entry
Database: PDB / ID: 4uml
TitleCrystal structure of ganglioside induced differentiation associated protein 2 (GDAP2) macro domain
ComponentsGANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 2
KeywordsSIGNALING PROTEIN / MACROD3
Function / homology
Function and homology information


response to retinoic acid / lysosomal membrane
Similarity search - Function
GDAP2, macro domain / Divergent CRAL/TRIO domain / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. ...GDAP2, macro domain / Divergent CRAL/TRIO domain / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ganglioside-induced differentiation-associated protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsElkins, J.M. / Wang, J. / Kopec, J. / Wang, D. / Strain-Damerell, C. / Shrestha, L. / Sieg, C. / Tallant, C. / Newman, J.A. / von Delft, F. ...Elkins, J.M. / Wang, J. / Kopec, J. / Wang, D. / Strain-Damerell, C. / Shrestha, L. / Sieg, C. / Tallant, C. / Newman, J.A. / von Delft, F. / Bountra, C. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Gdap2
Authors: Elkins, J.M. / Wang, J. / Knapp, S.
History
DepositionMay 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)25,5301
Polymers25,5301
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.840, 70.840, 97.549
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 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 2 / GDAP2


Mass: 25529.986 Da / Num. of mol.: 1 / Fragment: MACRO DOMAIN, RESIDUES 1-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NXN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.4 Å3/Da / Density % sol: 48.8 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG3350, 10% ETHYLENE GLYCOL, 0.2 M SODIUM/POTASSIUM TARTRATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→26.57 Å / Num. obs: 20255 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IQY

4iqy


Resolution: 1.9→57.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.791 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23089 993 4.9 %RANDOM
Rwork0.19608 ---
obs0.1978 19218 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.014 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--1.12 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 0 114 1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191595
X-RAY DIFFRACTIONr_bond_other_d0.0010.021515
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9672163
X-RAY DIFFRACTIONr_angle_other_deg0.81533486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75124.32867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24315272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.753158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
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_it2.5693.514804
X-RAY DIFFRACTIONr_mcbond_other2.5673.512803
X-RAY DIFFRACTIONr_mcangle_it3.85.2411002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0513.893791
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 70 -
Rwork0.294 1399 -
obs--99.8 %

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