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- PDB-3iqx: ADP complex of C.therm. Get3 in closed form -

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Basic information

Entry
Database: PDB / ID: 3iqx
TitleADP complex of C.therm. Get3 in closed form
ComponentsTail-anchored protein targeting factor Get3
KeywordsPROTEIN TRANSPORT / Protein targeting / ATPase / tail-anchored protein / Zn binding
Function / homology
Function and homology information


GET complex / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Arsenite translocating ATPase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBozkurt, G. / Wild, K. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural insights into tail-anchored protein binding and membrane insertion by Get3.
Authors: Bozkurt, G. / Stjepanovic, G. / Vilardi, F. / Amlacher, S. / Wild, K. / Bange, G. / Favaloro, V. / Rippe, K. / Hurt, E. / Dobberstein, B. / Sinning, I.
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail-anchored protein targeting factor Get3
B: Tail-anchored protein targeting factor Get3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2337
Polymers74,2652
Non-polymers9685
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-86 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.750, 105.590, 137.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA13 - 632 - 52
21SERSERTHRTHRBB13 - 632 - 52
12ASNASNPROPROAA68 - 9757 - 86
22ASNASNPROPROBB68 - 9757 - 86
13TYRTYRTHRTHRAA150 - 157139 - 146
23TYRTYRTHRTHRBB150 - 157139 - 146
14ARGARGPROPROAA232 - 337221 - 326
24ARGARGPROPROBB232 - 337221 - 326

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Components

#1: Protein Tail-anchored protein targeting factor Get3


Mass: 37132.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: Get3 / Plasmid: pet24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: G0SFE0*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.02M MgCl2, 0.1M Tris, 39% ethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 9088 / Num. obs: 9088 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.246 / Net I/σ(I): 6.56
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 3.4 % / Rsym value: 0.671 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AMPPNP complex of C. therm. Get3

Resolution: 3.5→49.28 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.803 / Occupancy max: 1 / Occupancy min: 1 / SU B: 83.047 / SU ML: 0.625 / Cross valid method: THROUGHOUT / ESU R Free: 0.731 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29518 455 5 %RANDOM
Rwork0.22874 ---
obs0.23202 8633 100 %-
all-9088 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 57 0 4178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224249
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0325746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32624.479192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.27115782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2331528
X-RAY DIFFRACTIONr_chiral_restr0.1080.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213116
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_it0.2041.52575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.37624188
X-RAY DIFFRACTIONr_scbond_it0.45931674
X-RAY DIFFRACTIONr_scangle_it0.7934.51558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A780tight positional0.060.05
B789loose positional0.095
A780tight thermal0.090.5
B789loose thermal0.110
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 34 -
Rwork0.289 635 -
obs--100 %
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)
13.0982-0.8187-0.9373.13410.35355.3091-0.0857-0.24290.04310.3580.06320.15290.03950.0560.02250.04820.005400.0193-0.00050.0534-19.5639-22.093416.391
22.032.30041.00616.82063.43687.03680.1631-0.05390.80280.0821-0.1691-0.4557-1.71030.74280.0060.6121-0.1894-0.01880.39820.08060.7826-10.6888-3.62292.4868
33.39211.53850.11154.81330.69482.67880.1314-0.24270.10760.4691-0.0656-0.0807-0.07590.0488-0.06580.32310.0447-0.03210.2636-0.04470.1003-11.0837-8.548539.6773
44.62862.4097-1.87733.6121.03454.9519-0.25530.63070.5566-0.61390.3218-0.1471-0.38660.274-0.06660.5256-0.0612-0.04070.5282-0.13230.60552.64376.513226.8683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 97
2X-RAY DIFFRACTION1A150 - 157
3X-RAY DIFFRACTION1A232 - 338
4X-RAY DIFFRACTION2A128 - 149
5X-RAY DIFFRACTION2A158 - 173
6X-RAY DIFFRACTION2A209 - 231
7X-RAY DIFFRACTION3B13 - 97
8X-RAY DIFFRACTION3B150 - 157
9X-RAY DIFFRACTION3B232 - 337
10X-RAY DIFFRACTION4B132 - 149
11X-RAY DIFFRACTION4B158 - 174
12X-RAY DIFFRACTION4B211 - 231

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