[English] 日本語
Yorodumi
- PDB-3ug7: Crystal Structure of Get3 from Methanocaldococcus jannaschii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ug7
TitleCrystal Structure of Get3 from Methanocaldococcus jannaschii
Componentsarsenical pump-driving ATPase
KeywordsHYDROLASE / tail-anchored / membrane protein / targeting factor / ATP-binding / GET3 / TRC40 / ATPase / ARSA / nucleotide-binding / protein targeting / protein transport
Function / homology
Function and homology information


arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
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 / Putative arsenical pump-driving ATPase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsSuloway, C.J.M. / Rome, M.E. / Clemons Jr., W.M.
CitationJournal: Embo J. / Year: 2012
Title: Tail-anchor targeting by a Get3 tetramer: the structure of an archaeal homologue.
Authors: Suloway, C.J. / Rome, M.E. / Clemons, W.M.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: arsenical pump-driving ATPase
B: arsenical pump-driving ATPase
C: arsenical pump-driving ATPase
D: arsenical pump-driving ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,97816
Polymers159,9104
Non-polymers2,06812
Water0
1
A: arsenical pump-driving ATPase
D: arsenical pump-driving ATPase
hetero molecules

A: arsenical pump-driving ATPase
D: arsenical pump-driving ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,97816
Polymers159,9104
Non-polymers2,06812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area24970 Å2
ΔGint-468 kcal/mol
Surface area48960 Å2
MethodPISA
2
B: arsenical pump-driving ATPase
C: arsenical pump-driving ATPase
hetero molecules

B: arsenical pump-driving ATPase
C: arsenical pump-driving ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,97816
Polymers159,9104
Non-polymers2,06812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area24760 Å2
ΔGint-466 kcal/mol
Surface area49090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.947, 149.636, 72.888
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-404-

ZN

21C-404-

ZN

31D-404-

ZN

-
Components

#1: Protein
arsenical pump-driving ATPase / ATPase Get3 / Arsenical resistance ATPase / Arsenite-translocating ATPase / Arsenite-transporting ATPase


Mass: 39977.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1142 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58542, EC: 3.6.3.16
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10% PEG3350, 0.2 M sodium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.736→149.636 Å / Num. all: 40502 / Num. obs: 24806

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.901→43.282 Å / SU ML: 0.99 / σ(F): 1.37 / Phase error: 33.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1254 5.06 %
Rwork0.2693 --
obs0.2706 24795 72.76 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.653 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7418 Å20 Å2-1.423 Å2
2--6.5896 Å20 Å2
3----1.8478 Å2
Refinement stepCycle: LAST / Resolution: 2.901→43.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9794 0 116 0 9910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910097
X-RAY DIFFRACTIONf_angle_d1.08613519
X-RAY DIFFRACTIONf_dihedral_angle_d15.2083973
X-RAY DIFFRACTIONf_chiral_restr0.071506
X-RAY DIFFRACTIONf_plane_restr0.0041699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-3.01690.4649110.4191282X-RAY DIFFRACTION8
3.0169-3.15420.449470.4049788X-RAY DIFFRACTION22
3.1542-3.32040.3759920.36931923X-RAY DIFFRACTION53
3.3204-3.52840.39041890.33813321X-RAY DIFFRACTION93
3.5284-3.80070.32281560.30323460X-RAY DIFFRACTION95
3.8007-4.18290.31191640.27383401X-RAY DIFFRACTION95
4.1829-4.78750.29131940.23963474X-RAY DIFFRACTION97
4.7875-6.02910.29951880.25883456X-RAY DIFFRACTION96
6.0291-43.28720.21232130.21943436X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.21643.5780.30144.33351.88597.45770.19741.3428-0.7185-0.26360.1666-1.30870.87091.0829-0.14310.60510.26040.19060.56150.12721.1626-17.756220.118-21.5573
24.86950.86960.20366.3858-0.55522.1592-0.5622-1.2942-0.11531.9179-0.4102-2.30820.22770.65350.4879-0.08950.6361.18980.5396-0.1287-0.7064-18.84721.843-3.1024
32.19713.00162.02342.00887.58856.95050.62360.122-0.71491.2332-0.2475-0.3691.47790.0216-0.26321.14470.0137-0.36450.2303-0.25691.0001-20.466843.83310.2176
41.5651-0.9597-1.73953.88540.86272.83650.0187-0.02750.53030.0323-0.0423-0.23970.23380.18060.02520.1415-0.0677-0.03340.23970.02180.334-29.031244.8708-5.4265
52.00672.60250.7329.86940.51742.0026-0.02580.60841.09070.516-0.0401-0.6863-0.85571.55970.1010.62870.0068-0.10260.86680.0131.0511-33.211979.1341-8.4833
65.14162.0323-0.87712.4253-1.51953.567-0.5523-0.08670.8254-0.8383-0.5691-0.4359-0.61590.49870.68540.53240.0399-0.09890.49960.1993-0.0206-26.616440.1404-15.7065
72.1778-1.6719-0.95988.6335-1.81172.7882-0.34260.6988-1.1841-0.78750.29751.22810.9968-0.8470.27170.9663-0.09840.27620.6512-0.36190.9136-38.126410.4064-12.7511
81.005-0.14030.03611.4488-0.05541.294-0.3468-0.581-1.16010.8067-0.2784-0.37580.63610.7390.26021.21560.30130.7576-0.1552-0.01471.3109-22.78917.3055-5.979
90.91680.2979-1.27580.2567-0.19262.0969-0.2239-0.1019-0.3513-0.09860.13891.34640.8707-1.4022-0.00760.3621-0.08160.39610.8759-0.11041.4475-26.113261.6027-34.4772
101.5896-0.5666-0.68235.0066-0.76626.715-0.4948-0.59940.05381.0581-0.66421.1049-0.3243-0.13510.83610.48240.1505-0.06110.7735-0.35570.8539-11.282968.3329-26.1191
113.04141.61052.29154.0165-2.21735.4205-0.161-0.71690.42420.4639-0.26710.5783-0.570.20030.4081.44990.31340.43540.829-0.13910.8054-0.593145.6619-17.9378
122.4596-1.05440.84012.7306-0.42890.9141-0.2334-0.4759-0.55240.5330.32480.55790.3789-0.4506-0.10740.5867-0.04490.08410.4310.09480.471-6.079645.2386-35.1475
132.60691.0329-0.55587.7094-0.89492.00221.1511-0.80020.17020.2489-0.05230.26690.4586-1.3628-1.14190.5170.0089-0.04890.82250.0931.2045-5.651611.03-40.3452
144.55860.0492-0.38083.2341.89914.0949-0.6276-0.3831-1.08360.8024-0.63161.57741.085-0.77120.54910.0211-0.0178-0.17280.54490.22460.8653-15.190450.0665-40.4312
153.2339-0.5067-3.47362.26460.71954.60120.41120.78241.4457-0.83060.3165-0.1841-0.67940.2363-1.1190.90420.0934-0.48070.61690.11541.0857-5.007279.7859-46.7079
162.48970.40620.51351.4081-1.45771.86030.0185-1.13331.07070.0933-0.30080.1118-0.8788-0.21360.27970.95920.19090.11310.4082-0.22691.2158-10.651682.8861-30.9461
176.0064-1.45281.12540.5387-0.07232.610.66641.0189-0.2418-0.6718-0.30561.74060.3747-0.322-0.30241.039-0.2203-0.18120.5467-0.06661.9307-14.1577-14.1445-41.3793
180.98521.4106-0.26653.5183-0.81461.4521-0.05990.20650.06630.3775-0.1517-0.0095-0.2907-0.08530.26171.9538-0.1105-0.10891.21220.12781.5789-6.43928.1301-53.1067
191.66960.29330.70762.84770.35613.1528-0.0911-0.1065-0.5310.43350.09920.97740.2926-0.64680.03640.5576-0.01290.30750.39630.08160.7725-5.94998.6904-34.8068
208.27042.5775-1.17656.388-3.89717.742-0.5380.884-0.3152-0.07730.85651.19320.6826-1.0821-0.32370.89060.01320.31470.70950.14130.6619-3.872742.729-30.1175
212.6973-1.11930.69812.91610.24583.98660.07580.1168-0.5354-0.0973-0.48011.0417-0.1609-1.28540.09640.7698-0.16030.76440.44890.18781.1015-12.95343.908-26.9252
221.25583.0681-0.28047.7727-1.01130.79630.102-0.0104-1.58391.48870.25620.45561.44010.07160.41131.1461-0.0570.22350.79720.02211.322-1.4697-25.8212-24.0929
231.28110.8180.28521.7661-0.20840.89440.70680.4816-0.5039-0.34310.16350.50080.1969-0.1361-0.82381.6107-0.2666-0.28110.48620.18152.2077-11.8116-28.893-37.2885
243.71630.7415-0.82690.71630.97265.1648-0.32571.30960.559-1.5166-0.4333-0.6674-1.309-0.44760.42791.6370.18290.27890.89910.3771.224-27.7297104.107-15.4981
252.9624-0.01860.60169.8784-1.09489.45920.54060.7568-0.0070.40380.38240.3255-0.7224-0.2309-0.86070.611-0.1301-0.22950.82690.20351.0036-41.425681.4886-18.1246
261.529-0.61110.47652.29470.15961.5530.15250.36790.5311-0.2631-0.2661-0.4159-0.52220.22150.12040.8078-0.05590.05340.37340.09230.9644-28.768581.2337-5.0206
272.01092.2563-3.3678.37244.13925.3706-0.14041.01380.29-0.34350.2697-0.02410.3843-0.4539-0.18390.6352-0.1098-0.23660.50860.15220.383-26.818947.21520.0293
283.1291-0.9367-0.01632.93511.89845.36660.40610.65840.548-0.5787-0.627-1.1519-0.17140.60590.14240.5138-0.10870.22580.39040.30311.2162-18.186986.0545-4.5241
290.19810.4538-0.47255.4978-1.34541.41890.6224-0.45321.19710.4208-0.1517-1.1945-1.25940.0664-0.40341.1399-0.27380.04780.7057-0.03591.5297-24.2887115.80625.6096
301.4407-0.99120.39381.82470.31460.39430.43440.63830.1856-0.4455-0.35240.0232-0.5242-0.0148-0.0722.2617-0.32210.06780.58470.53951.7138-26.4958118.8719-11.0019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:27)
2X-RAY DIFFRACTION2(chain A and resid 28:94)
3X-RAY DIFFRACTION3(chain A and resid 95:111)
4X-RAY DIFFRACTION4(chain A and resid 112:192)
5X-RAY DIFFRACTION5(chain A and resid 193:202)
6X-RAY DIFFRACTION6(chain A and resid 210:244)
7X-RAY DIFFRACTION7(chain A and resid 245:308)
8X-RAY DIFFRACTION8(chain A and resid 309:333)
9X-RAY DIFFRACTION9(chain B and resid 22:27)
10X-RAY DIFFRACTION10(chain B and resid 28:94)
11X-RAY DIFFRACTION11(chain B and resid 95:111)
12X-RAY DIFFRACTION12(chain B and resid 112:192)
13X-RAY DIFFRACTION13(chain B and resid 193:202)
14X-RAY DIFFRACTION14(chain B and resid 210:244)
15X-RAY DIFFRACTION15(chain B and resid 245:308)
16X-RAY DIFFRACTION16(chain B and resid 309:333)
17X-RAY DIFFRACTION17(chain C and resid 26:94)
18X-RAY DIFFRACTION18(chain C and resid 95:111)
19X-RAY DIFFRACTION19(chain C and resid 112:192)
20X-RAY DIFFRACTION20(chain C and resid 193:202)
21X-RAY DIFFRACTION21(chain C and resid 210:244)
22X-RAY DIFFRACTION22(chain C and resid 245:308)
23X-RAY DIFFRACTION23(chain C and resid 309:333)
24X-RAY DIFFRACTION24(chain D and resid 26:94)
25X-RAY DIFFRACTION25(chain D and resid 95:111)
26X-RAY DIFFRACTION26(chain D and resid 112:192)
27X-RAY DIFFRACTION27(chain D and resid 193:202)
28X-RAY DIFFRACTION28(chain D and resid 210:244)
29X-RAY DIFFRACTION29(chain D and resid 245:308)
30X-RAY DIFFRACTION30(chain D and resid 309:333)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more