[English] 日本語
Yorodumi
- PDB-7ppv: Structure of diFe-Sulerythrin at 2.70 MGy total absorbed dose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ppv
TitleStructure of diFe-Sulerythrin at 2.70 MGy total absorbed dose
ComponentsSulerythrin
KeywordsELECTRON TRANSPORT / radiation damage / spatially resolved anomalous dispersion refinement / redox reaction
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
: / Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / HYDROXIDE ION / Sulerythrin
Similarity search - Component
Biological speciesSulfurisphaera tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsLennartz, F. / Weiss, M.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390540038 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Determining the oxidation state of elements by X-ray crystallography.
Authors: Lennartz, F. / Jeoung, J.H. / Ruenger, S. / Dobbek, H. / Weiss, M.S.
History
DepositionSep 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Sulerythrin
B: Sulerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,52410
Polymers32,1962
Non-polymers3288
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-143 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.150, 72.150, 97.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

21A-479-

HOH

31A-480-

HOH

41B-653-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 4 or resid 6...
21(chain B and (resid 3 through 4 or resid 6...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 4 or resid 6...A3 - 4
121(chain A and (resid 3 through 4 or resid 6...A6 - 7
131(chain A and (resid 3 through 4 or resid 6...A9 - 10
141(chain A and (resid 3 through 4 or resid 6...A0
151(chain A and (resid 3 through 4 or resid 6...A66
161(chain A and (resid 3 through 4 or resid 6...A1 - 601
171(chain A and (resid 3 through 4 or resid 6...A96 - 107
181(chain A and (resid 3 through 4 or resid 6...A1
191(chain A and (resid 3 through 4 or resid 6...A1 - 601
1101(chain A and (resid 3 through 4 or resid 6...A129 - 1
1111(chain A and (resid 3 through 4 or resid 6...A139 - 141
1121(chain A and (resid 3 through 4 or resid 6...A1 - 601
1131(chain A and (resid 3 through 4 or resid 6...A139 - 141
1141(chain A and (resid 3 through 4 or resid 6...A201 - 401
1151(chain A and (resid 3 through 4 or resid 6...A601
211(chain B and (resid 3 through 4 or resid 6...B3 - 4
221(chain B and (resid 3 through 4 or resid 6...B6 - 7
231(chain B and (resid 3 through 4 or resid 6...B9 - 10
241(chain B and (resid 3 through 4 or resid 6...B1 - 601
251(chain B and (resid 3 through 4 or resid 6...B1 - 601
261(chain B and (resid 3 through 4 or resid 6...B49 - 64
271(chain B and (resid 3 through 4 or resid 6...B1 - 601
281(chain B and (resid 3 through 4 or resid 6...B121 - 127
291(chain B and (resid 3 through 4 or resid 6...B129 - 134
2101(chain B and (resid 3 through 4 or resid 6...B136 - 137
2111(chain B and (resid 3 through 4 or resid 6...B139 - 401
2121(chain B and (resid 3 through 4 or resid 6...B601

-
Components

#1: Protein Sulerythrin


Mass: 16098.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii str. 7 (archaea)
Gene: ST2370, STK_23700 / Production host: Escherichia coli (E. coli) / References: UniProt: F9VPE5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-Tris 24% (w/v) PEG 3350 pH 5.5 Sulerythrin at 14.00 mg/ml

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2021
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.36→38.553 Å / Num. obs: 122036 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 13.8
Reflection shellResolution: 1.36→1.4 Å / Num. unique obs: 8996 / CC1/2: 0.99 / Rpim(I) all: 0.479 / Rrim(I) all: 1.677

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J30

1j30


Resolution: 1.36→38.553 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 6089 4.99 %
Rwork0.1808 115932 -
obs0.1817 122021 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.56 Å2 / Biso mean: 24.5885 Å2 / Biso min: 10.69 Å2
Refinement stepCycle: final / Resolution: 1.36→38.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 12 351 2603
Biso mean--29.72 32.39 -
Num. residues----283
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1072X-RAY DIFFRACTION4.435TORSIONAL
12B1072X-RAY DIFFRACTION4.435TORSIONAL
LS refinement shellHighest resolution: 1.36 Å
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)
10.0768-0.0059-0.01720.0834-0.10310.09610.0227-0.09090.00770.210.2039-0.18320.27320.295-0.00090.3152-0.021-0.01060.4823-0.05060.411834.3806-33.77520.3467
20.85920.0790.29910.69870.2181.2318-0.01760.03150.056-0.03380.0213-0.1045-0.0090.016-00.1391-0.00210.02510.13020.00560.139613.2754-30.590318.6877
30.7624-0.5550.33611.5243-0.46250.75920.0136-0.06570.12890.13010.03870.0511-0.0445-0.00140.00270.15630.0037-0.00340.1441-0.02240.15575.8845-20.174333.0108
40.5016-0.03140.14830.20630.15420.88780.140.0223-0.0692-0.4516-0.16880.8692-0.7395-0.3455-0.02350.40870.0726-0.0430.2190.03730.45531.9488-6.386916.0232
51.0722-0.6980.06722.0949-0.64130.86990.02220.00690.0633-0.0107-0.0362-0.1330.01540.0472-00.127-0.00510.00090.1293-0.01140.10468.1849-29.33923.858
60.3557-0.2401-0.65090.31790.2450.4461-0.00730.17550.3387-0.17350.0681-0.07-0.1931-0.0175-0.00430.2358-0.01420.02810.22070.03190.19419.3928-21.43274.6598
70.7616-0.0270.64930.37140.28731.2978-0.03780.14150.3385-0.1490.0496-0.4069-0.2630.3272-0.03950.1629-0.01660.06520.34590.0240.290930.5798-29.90637.5028
81.58790.24740.27520.77740.43331.08070.02180.3912-0.349-0.2490.0191-0.09870.12380.09020.01210.1747-0.01690.05550.22560.01210.141315.3132-33.15171.2257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )A1 - 7
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 97 )A8 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 142 )A98 - 142
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )B1 - 7
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 66 )B8 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 97 )B67 - 97
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 112 )B98 - 112
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 141 )B113 - 141

+
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