[English] 日本語
Yorodumi
- PDB-7zpw: Crystal structure of Pizza6-TSK-TSH with Silicotungstic Acid (STA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zpw
TitleCrystal structure of Pizza6-TSK-TSH with Silicotungstic Acid (STA) polyoxometalate
ComponentsPizza6-TSK-TSH
KeywordsUNKNOWN FUNCTION / beta propeller / synthetic / designer / polyoxometalate / STA / co-crystal / silicotungstic acid
Function / homologyKeggin (STA)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S89918N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: To be published
Title: Mutational study of a symmetry matched protein-polyoxometalate interface.
Authors: Wouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pizza6-TSK-TSH
D: Pizza6-TSK-TSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3973
Polymers51,5232
Non-polymers2,8741
Water5,062281
1
A: Pizza6-TSK-TSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6362
Polymers25,7611
Non-polymers2,8741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Pizza6-TSK-TSH


Theoretical massNumber of molelcules
Total (without water)25,7611
Polymers25,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.777, 44.904, 119.921
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pizza6-TSK-TSH


Mass: 25761.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SIW / Keggin (STA)


Mass: 2874.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O40SiW12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.47 % / Mosaicity: 0.09 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→39.97 Å / Num. obs: 37885 / % possible obs: 98.2 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.031 / Rrim(I) all: 0.108 / Net I/σ(I): 16.6 / Num. measured all: 488930 / Scaling rejects: 547
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.849.60.2261931220220.990.0750.2396.592.5
9-39.977.50.10320762780.9480.050.11720.184.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.23 Å39.97 Å
Translation4.23 Å39.97 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WW9

3ww9


Resolution: 1.8→39.97 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 3947 5.38 %
Rwork0.1943 69446 -
obs0.196 37885 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.06 Å2 / Biso mean: 22.4857 Å2 / Biso min: 7.51 Å2
Refinement stepCycle: final / Resolution: 1.8→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 212 301 4040
Biso mean--20.21 28.83 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.33151580.30162164232291
1.82-1.850.30021900.28762299248992
1.85-1.870.29931320.26532410254293
1.87-1.890.20781990.22642278247794
1.89-1.920.28791220.24352453257595
1.92-1.950.32771240.22882567269197
1.95-1.980.20991410.21362376251797
1.98-2.010.2581380.20882520265898
2.01-2.050.31251860.17512536272298
2.05-2.090.2221560.18632354251099
2.09-2.130.26151140.19822583269799
2.13-2.170.2361190.20422557267699
2.17-2.220.29121760.18472398257499
2.22-2.270.15111390.17552524266399
2.27-2.320.31221000.1932495259599
2.32-2.390.23411240.18812628275299
2.39-2.460.28281260.19992564269099
2.46-2.540.20371260.21382464259099
2.54-2.630.26741310.18572617274899
2.63-2.730.22731980.19792429262799
2.73-2.860.18561140.19892564267899
2.86-3.010.20271410.212525882729100
3.01-3.20.30651400.196125112651100
3.2-3.440.25131280.187125252653100
3.44-3.790.2611120.190825592671100
3.79-4.330.16251490.169725302679100
4.34-5.450.15951250.151225462671100
5.46-39.970.16691390.20632407254694
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)
10.2555-0.1332-0.20480.53990.38891.28880.0471-0.2553-0.18730.03160.2203-0.03680.78670.25080.7030.1757-0.0268-0.0676-0.0321-0.0220.128-12.09352.070215.318
20.67620.23450.05740.3669-0.24821.60740.08670.112-0.07250.0680.1079-0.0819-0.20940.49010.57440.0865-0.03130.03420.1156-0.0370.1209-4.392817.942615.1359
30.4715-0.30240.42890.5687-0.01931.61430.2253-0.14930.0336-0.01630.04740.0978-0.156-0.69720.74930.05480.07790.00920.07290.0510.1319-22.121117.02214.9533
40.9367-0.23340.0210.2953-0.47511.24260.1522-0.1565-0.1471-0.19120.04030.0130.61420.22540.4990.16340.0517-0.06340.09580.00190.137-8.12481.586244.2786
50.64090.25380.21260.2104-0.11621.25860.07350.2109-0.2022-0.15840.13820.03290.5598-0.10550.74610.1151-0.1409-0.05460.07330.06330.1488-19.29872.583544.7523
60.63740.2296-0.2490.17860.23671.820.3182-0.0390.05050.00690.02910.0975-0.0491-0.70581.02920.05350.00620.010.20010.06570.1408-24.804312.959444.7801
70.2028-0.1116-0.18930.9979-0.41721.51050.01450.1736-0.0124-0.2280.19640.0948-0.2695-0.40661.1420.21670.0650.0848-0.0174-0.0280.1405-18.40122.920444.7564
80.28060.15570.46690.95150.03252.05920.03640.19230.18730.17560.3185-0.0891-0.66740.45650.93830.1432-0.06520.04630.0199-0.08430.1192-6.748522.393644.9541
90.6112-0.2066-0.16370.147-0.08140.88180.2310.05260.2428-0.04890.0806-0.126-0.23940.53030.8592-0.08370.063-0.14780.2198-0.08530.1038-1.177411.907645.2275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 82 )A2 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 166 )A83 - 166
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 252 )A167 - 252
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 40 )D2 - 40
5X-RAY DIFFRACTION5chain 'D' and (resid 41 through 82 )D41 - 82
6X-RAY DIFFRACTION6chain 'D' and (resid 83 through 124 )D83 - 124
7X-RAY DIFFRACTION7chain 'D' and (resid 125 through 166 )D125 - 166
8X-RAY DIFFRACTION8chain 'D' and (resid 167 through 208 )D167 - 208
9X-RAY DIFFRACTION9chain 'D' and (resid 209 through 252 )D209 - 252

+
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