[English] 日本語
Yorodumi
- PDB-3wco: Crystal structure of the depentamerized mutant of N-terminal trun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wco
TitleCrystal structure of the depentamerized mutant of N-terminal truncated selenocysteine synthase SelA
ComponentsL-seryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / Fold-type-I pyridoxal 5'-phosphate (PLP) dependent enzyme / homodimer / L-seryl-tRNA(Sec) selenium transferase / selenocysteine synthesis / selenium metabolism
Function / homology
Function and homology information


L-seryl-tRNASec selenium transferase / L-seryl-tRNA(Sec) selenium transferase activity / selenocysteine incorporation / identical protein binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #180 / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aspartate Aminotransferase, domain 1 - #180 / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOSULFATE / L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Dimer-Dimer Interaction of the Bacterial Selenocysteine Synthase SelA Promotes Functional Active-Site Formation and Catalytic Specificity
Authors: Itoh, Y. / Brocker, M.J. / Sekine, S. / Soll, D. / Yokoyama, S.
History
DepositionMay 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: 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_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5087
Polymers88,9472
Non-polymers5615
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-36 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.190, 81.286, 95.537
Angle α, β, γ (deg.)90.000, 92.230, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein L-seryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase


Mass: 44473.449 Da / Num. of mol.: 2 / Fragment: UNP residues 62-452 / Mutation: T191Y, T192Y, D199R, Y220P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1031, selA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O67140, L-seryl-tRNASec selenium transferase
#2: Chemical
ChemComp-THJ / THIOSULFATE / Thiosulfate


Mass: 112.128 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O3S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM sodium MES-HCl, 2.5% PEG4000, 150mM Na2S2O3, 70mM NaNO3, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 35599 / Num. obs: 35457 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 49.31 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3520 / Rsym value: 0.561 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1I

3w1i


Resolution: 2.4→41.161 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8229 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1770 5.01 %Random
Rwork0.1788 ---
obs0.1813 35363 99.14 %-
all-35670 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.3 Å2 / Biso mean: 64.5454 Å2 / Biso min: 25.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 25 105 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086146
X-RAY DIFFRACTIONf_angle_d1.1478265
X-RAY DIFFRACTIONf_chiral_restr0.07952
X-RAY DIFFRACTIONf_plane_restr0.0041043
X-RAY DIFFRACTIONf_dihedral_angle_d14.9962393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46180.2891410.23232500264197
2.4618-2.53430.2861300.22192560269099
2.5343-2.6160.31011400.22592579271999
2.616-2.70950.32471350.219225902725100
2.7095-2.8180.29091360.215925792715100
2.818-2.94620.2851310.202825842715100
2.9462-3.10150.23691430.190425832726100
3.1015-3.29570.28221340.193726172751100
3.2957-3.55010.24481290.190526012730100
3.5501-3.90710.23011370.169826022739100
3.9071-4.47180.21461280.158426132741100
4.4718-5.63180.19661470.15642600274799
5.6318-41.16660.17031390.16362585272496
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)
12.82191.40850.06832.51480.75860.88670.0962-0.42040.02710.1578-0.07750.178-0.0372-0.111-0.02990.25010.0677-0.00960.48240.03670.283311.2802-21.259532.969
21.23560.02740.01043.24391.23792.934-0.08560.2389-0.386-0.90580.18740.0388-0.0338-0.0874-0.10030.5945-0.0163-0.00120.3105-0.02190.409918.4325-31.64896.9291
31.6113-0.0931-1.21082.45870.76693.6928-0.16770.0462-0.5818-0.55640.2196-0.13640.6707-0.0515-0.0620.6856-0.01540.00230.3485-0.02880.572221.3876-43.03679.1914
42.28920.0328-0.27853.25020.85453.4762-0.04230.0381-0.5299-0.41940.199-0.26810.48060.0107-0.10430.38480.0469-0.03030.2601-0.03690.383122.2516-34.86616.1645
51.4540.3250.02593.70980.08682.1956-0.0044-0.1604-0.2331-0.10170.0927-0.2995-0.21060.1009-0.09720.28320.0630.00920.3781-0.03060.322622.1599-22.3823.3114
65.51210.571-0.08523.3252-1.3180.8838-0.3753-0.5261-0.33670.82190.1559-0.1390.0032-0.0525-0.03070.51050.0831-0.00740.50920.13390.556217.1451-38.095634.9658
76.8553-1.5535-1.60262.3775-0.20683.2023-0.3647-0.1507-0.61930.2827-0.09360.40770.5081-0.33440.05490.60750.02950.07620.8060.34260.70850.3789-46.185843.6841
83.46530.1513-1.28262.12240.29112.6262-0.07230.0381-0.5759-0.08880.12130.4510.3981-0.64770.06340.5044-0.0446-0.03080.65240.22080.8615-3.6262-44.473733.5339
95.990.52140.10294.411-0.053.0051-0.0352-0.7343-0.26750.08170.1540.8111-0.0405-0.93770.08030.34330.0491-0.03610.76730.18460.7817-13.314-30.709834.9721
104.5949-1.3071-0.48323.0920.29872.8912-0.2347-0.8006-0.49840.10550.10350.40690.0616-0.46440.03230.4311-0.05070.02770.72280.24260.7438-5.9403-36.704338.8997
112.63741.53980.2782.76690.12541.09080.0056-0.4747-0.01110.02440.03060.22520.0551-0.1874-0.05120.31470.09340.02740.46390.03180.302713.868-17.270230.38
121.99450.33840.05592.9124-0.86393.2673-0.06830.20790.204-0.94850.02060.2444-0.05750.0781-0.0060.64660.0014-0.08960.28910.0210.40512.5304-7.31828.0655
133.24530.15770.57932.1621-1.10432.3849-0.04180.35950.6538-0.8501-0.00640.201-0.17310.13680.06370.95080.0084-0.06270.44170.06390.639614.15084.1983-1.1896
142.3149-0.24331.04372.2219-1.32862.85230.02120.07390.6477-0.49050.22610.5941-0.71240.02560.01390.70710.0619-0.12090.33140.02640.68337.84955.29599.8047
152.2185-0.22530.12062.9641-0.47672.9276-0.0324-0.24180.4316-0.41730.1290.5905-0.2205-0.1066-0.06610.37010.0647-0.05440.3523-0.01370.42767.5276-7.201218.8006
163.95880.03362.02731.51841.10631.7496-0.1193-0.97160.6320.1605-0.01260.2033-0.2253-0.27190.09540.48660.10.07570.6785-0.260.556821.12913.993339.4832
173.4972-0.21741.06242.70590.84531.92830.0058-0.47630.60730.01120.156-0.366-0.27480.1396-0.08270.38740.00640.07190.4948-0.15810.459337.03520.314835.8557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 111 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 217 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 259 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 307 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 332 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 333 through 348 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 349 through 362 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 363 through 399 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 400 through 420 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 421 through 452 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 123 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 189 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 190 through 217 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 226 through 259 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 332 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 333 through 363 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 364 through 452 )B0

+
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