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- PDB-2woo: Nucleotide-free form of S. pombe Get3 -

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Basic information

Entry
Database: PDB / ID: 2woo
TitleNucleotide-free form of S. pombe Get3
ComponentsATPASE GET3
KeywordsHYDROLASE / TAIL-ANCHORED / MEMBRANE PROTEIN / TARGETING FACTOR / ENDOPLASMIC RETICULUM / GET3 / ATPASE / TRC40 / ATP-BINDING / GOLGI APPARATUS / ER-GOLGI TRANSPORT / NUCLEOTIDE-BINDING / ARSENICAL RESISTANCE / NUCLEUS / CYTOPLASM / TRANSPORT / ARSA / ARSENITE
Function / homology
Function and homology information


GET complex / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol
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
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.006 Å
AuthorsMateja, A. / Szlachcic, A. / Downing, M.E. / Dobosz, M. / Mariappan, M. / Hegde, R.S. / Keenan, R.J.
CitationJournal: Nature / Year: 2009
Title: The Structural Basis of Tail-Anchored Membrane Protein Recognition by Get3.
Authors: Mateja, A. / Szlachcic, A. / Downing, M.E. / Dobosz, M. / Mariappan, M. / Hegde, R.S. / Keenan, R.J.
History
DepositionJul 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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: ATPASE GET3
B: ATPASE GET3
C: ATPASE GET3
D: ATPASE GET3
E: ATPASE GET3
F: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,6829
Polymers219,4856
Non-polymers1963
Water0
1
A: ATPASE GET3
B: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2273
Polymers73,1622
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATPASE GET3
D: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2273
Polymers73,1622
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ATPASE GET3
F: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2273
Polymers73,1622
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-52 kcal/mol
Surface area74180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.795, 92.922, 286.468
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-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
311CHAIN C
411CHAIN D
511CHAIN E
611CHAIN F

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Components

#1: Protein
ATPASE GET3 / GET3 / ARR4 / TRC40 / ASNA-1 / ATPASE SUBUNIT OF THE GET COMPLEX / ARSENICAL PUMP-DRIVING ATPASE / ...GET3 / ARR4 / TRC40 / ASNA-1 / ATPASE SUBUNIT OF THE GET COMPLEX / ARSENICAL PUMP-DRIVING ATPASE / ARSENITE-TRANSLOCATING ATPASE / ARSENICAL RESISTANCE ATPASE / ARSENITE-TRANSPORTING ATPASE


Mass: 36580.879 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)/PLYSS / References: UniProt: Q9P7F8, EC: 3.6.3.16
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% PEG 3350, 0.1 M MES PH 6.5, 0.4 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 37723 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.7 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOMER OF PDB ENTRY 2WOJ

2woj


Resolution: 3.006→40.687 Å / SU ML: 1 / σ(F): 1.34 / Phase error: 30.27 / Stereochemistry target values: ML
Details: ELECTRON DENSITY IS WEAKEST IN THE HELICAL SUBDOMAINS. DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.288 1890 5 %
Rwork0.2373 --
obs0.2397 37721 93.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.142 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso mean: 120.52 Å2
Baniso -1Baniso -2Baniso -3
1--19.0285 Å20 Å20 Å2
2--9.7905 Å2-0 Å2
3---7.845 Å2
Refinement stepCycle: LAST / Resolution: 3.006→40.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14112 0 3 0 14115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814358
X-RAY DIFFRACTIONf_angle_d1.03219368
X-RAY DIFFRACTIONf_dihedral_angle_d18.975376
X-RAY DIFFRACTIONf_chiral_restr0.0662238
X-RAY DIFFRACTIONf_plane_restr0.0042478
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2352X-RAY DIFFRACTIONPOSITIONAL
12B2352X-RAY DIFFRACTIONPOSITIONAL0.035
13C2352X-RAY DIFFRACTIONPOSITIONAL0.038
14D2352X-RAY DIFFRACTIONPOSITIONAL0.035
15E2352X-RAY DIFFRACTIONPOSITIONAL0.037
16F2352X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0056-3.08080.38541000.36342015X-RAY DIFFRACTION75
3.0808-3.1640.37211120.3242327X-RAY DIFFRACTION87
3.164-3.25710.361340.32572389X-RAY DIFFRACTION89
3.2571-3.36220.31131240.30942456X-RAY DIFFRACTION90
3.3622-3.48230.33911390.29172448X-RAY DIFFRACTION92
3.4823-3.62160.32621220.26862491X-RAY DIFFRACTION93
3.6216-3.78630.30331240.25592546X-RAY DIFFRACTION94
3.7863-3.98580.29471540.23362603X-RAY DIFFRACTION96
3.9858-4.23530.26781430.23922688X-RAY DIFFRACTION99
4.2353-4.56190.28171560.20722706X-RAY DIFFRACTION100
4.5619-5.02020.2621570.18942718X-RAY DIFFRACTION100
5.0202-5.74490.25141270.20352779X-RAY DIFFRACTION100
5.7449-7.23130.24621500.22252785X-RAY DIFFRACTION100
7.2313-40.69020.25531480.20062880X-RAY DIFFRACTION98
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)
12.8863-0.31721.31570.83060.45291.8690.109-0.2575-0.0160.09550.0048-0.0526-0.180.0848-00.81020.00370.06580.6494-0.13650.515425.498726.733738.45
21.0998-0.22010.37393.47391.42332.0003-0.278-0.1384-0.120.19470.4170.23790.1369-0.0331-00.7860.0518-0.01750.89660.04140.504935.9284-0.797958.9086
32.0957-0.43251.58971.5797-1.10663.64490.33470.0899-0.2768-0.0972-0.06180.14640.59940.271600.58320.1175-0.08680.4463-0.1260.471525.49888.19596.3327
40.49870.7885-2.19921.3024-2.47996.3420.0930.2668-0.341-0.05510.42730.5941-0.0293-1.0062-00.7787-0.0103-0.17040.82290.05611.0222-8.3574-4.97648.8724
52.82872.2804-1.94672.4927-2.0583.35850.0834-0.148-0.17850.36930.1490.30150.1814-0.3867-00.98420.0625-0.15580.7175-0.05610.83361.0189-34.68229.5306
61.50770.5114-0.71783.2432-0.13122.1701-0.1718-0.50260.0470.20.29950.14250.14350.215100.99370.1212-0.02891.26030.06531.0607-0.7872-18.453761.0351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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