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- PDB-1o3x: Crystal structure of human GGA1 GAT domain -

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Basic information

Entry
Database: PDB / ID: 1o3x
TitleCrystal structure of human GGA1 GAT domain
ComponentsADP-ribosylation factor binding protein GGA1
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process / protein localization / trans-Golgi network / small GTPase binding / positive regulation of protein catabolic process / early endosome membrane / early endosome / endosome membrane / Amyloid fiber formation / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / ENTH/VHS / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsShiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Molecular Mechanism of Membrane Recruitment of Gga by Arf in Lysosomal Protein Transport
Authors: Shiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
History
DepositionMay 8, 2003Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 20, 2003ID: 1J2H
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ADP-ribosylation factor binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)16,0001
Polymers16,0001
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.110, 85.110, 59.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ADP-ribosylation factor binding protein GGA1


Mass: 16000.128 Da / Num. of mol.: 1 / Fragment: Gat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UJY5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.96 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, PEG6000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9500, 0.9806, 0.9808, 1.0
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2001
RadiationMonochromator: SI (111) + GE (220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.98061
30.98081
411
ReflectionResolution: 2.1→30 Å / Num. all: 9302 / Num. obs: 9301 / % possible obs: 100 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.056 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28951 443 4.8 %RANDOM
Rwork0.24477 ---
all0.2468 9301 --
obs0.2468 8858 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 0 108 994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.9751193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4263111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84415184
X-RAY DIFFRACTIONr_chiral_restr0.1260.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02660
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2810.3445
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2740.549
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.328
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1591.5557
X-RAY DIFFRACTIONr_mcangle_it2.1282892
X-RAY DIFFRACTIONr_scbond_it3.1273334
X-RAY DIFFRACTIONr_scangle_it5.3744.5301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 35
Rwork0.263 673

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