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- PDB-2a7b: On the Routine Use of Soft X-Rays in Macromolecular Crystallograp... -

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Basic information

Entry
Database: PDB / ID: 2a7b
TitleOn the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The Optimal Data Collection Wavelength
Componentsgamma-adaptin appendage domain
KeywordsENDOCYTOSIS/EXOCYTOSIS / Protein transport / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


basolateral protein secretion / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle ...basolateral protein secretion / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle / clathrin-coated pit / vesicle-mediated transport / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / presynapse / early endosome / lysosomal membrane / perinuclear region of cytoplasm
Similarity search - Function
Gamma-adaptin ear (GAE) domain / Adaptor protein complex AP-1, gamma subunit / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region ...Gamma-adaptin ear (GAE) domain / Adaptor protein complex AP-1, gamma subunit / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
XENON / AP-1 complex subunit gamma-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsMueller-Dieckmann, C. / Panjikar, S. / Tucker, P.A. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Tucker, P.A. / Weiss, M.S.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gamma-adaptin appendage domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6803
Polymers13,4171
Non-polymers2632
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.430, 53.760, 66.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein gamma-adaptin appendage domain


Mass: 13417.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1g1, Adtg, Clapg1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22892
#2: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.24 Å3/Da / Density % sol: 44.99 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.8
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 14704

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.747 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 293 2 %RANDOM
Rwork0.182 ---
obs0.183 14704 99.9 %-
all-15011 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.6 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 2 87 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022966
X-RAY DIFFRACTIONr_bond_other_d0.0010.02877
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9551315
X-RAY DIFFRACTIONr_angle_other_deg0.87732060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09425.85441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63915171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.335153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02173
X-RAY DIFFRACTIONr_nbd_refined0.2160.2195
X-RAY DIFFRACTIONr_nbd_other0.20.21078
X-RAY DIFFRACTIONr_nbtor_refined0.20.2518
X-RAY DIFFRACTIONr_nbtor_other0.1070.2735
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.8380.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3361.5606
X-RAY DIFFRACTIONr_mcbond_other0.2851.5237
X-RAY DIFFRACTIONr_mcangle_it2.7262.51000
X-RAY DIFFRACTIONr_scbond_it5.2195367
X-RAY DIFFRACTIONr_scangle_it9.07110315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 24 -
Rwork0.204 1015 -
obs--100 %

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