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- PDB-7ppu: Structure of diFe-Sulerythrin at 0.57 MGy total absorbed dose -

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Basic information

Entry
Database: PDB / ID: 7ppu
TitleStructure of diFe-Sulerythrin at 0.57 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: 1.34 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulerythrin
B: Sulerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,66710
Polymers32,3382
Non-polymers3288
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-144 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.020, 72.020, 97.997
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-475-

HOH

21B-642-

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 - 21
141(chain A and (resid 3 through 4 or resid 6...A23 - 45
151(chain A and (resid 3 through 4 or resid 6...A49 - 64
161(chain A and (resid 3 through 4 or resid 6...A66 - 107
171(chain A and (resid 3 through 4 or resid 6...A109 - 119
181(chain A and (resid 3 through 4 or resid 6...A121 - 127
191(chain A and (resid 3 through 4 or resid 6...A129 - 134
1101(chain A and (resid 3 through 4 or resid 6...A136 - 142
1111(chain A and (resid 3 through 4 or resid 6...A201 - 601
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...B0
241(chain B and (resid 3 through 4 or resid 6...B0 - 64
251(chain B and (resid 3 through 4 or resid 6...B66 - 107
261(chain B and (resid 3 through 4 or resid 6...B19 - 119
271(chain B and (resid 3 through 4 or resid 6...B0 - 601
281(chain B and (resid 3 through 4 or resid 6...B0 - 601
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 - 601

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Components

#1: Protein Sulerythrin


Mass: 16169.155 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.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.89 %
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

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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: Nov 17, 2020
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: 1.34→38.531 Å / Num. obs: 126860 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.07 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.037 / Rrim(I) all: 0.124 / Net I/σ(I): 8
Reflection shellResolution: 1.34→1.42 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 20266 / CC1/2: 0.55 / Rpim(I) all: 0.337 / Rrim(I) all: 1.083 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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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: 1.34→38.531 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 2100 1.66 %
Rwork0.1852 124739 -
obs0.1857 126839 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 20.6713 Å2 / Biso min: 8.61 Å2
Refinement stepCycle: final / Resolution: 1.34→38.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 10 340 2608
Biso mean--21.79 29.82 -
Num. residues----287
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1152X-RAY DIFFRACTION4.584TORSIONAL
12B1152X-RAY DIFFRACTION4.584TORSIONAL
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)
10.2024-0.20260.04310.444-0.03270.339-0.0632-0.03780.12450.04130.04730.1186-0.0695-0.02820.03580.12740.01140.02260.1276-0.00330.1241-15.0598-28.5959-15.2087
20.40360.056-0.02370.5027-0.09480.2579-0.0028-0.03030.07070.00960.00960.10880.023-0.0260.00020.1080.00010.00870.1038-0.00370.1242-13.1169-27.3012-24.3715
30.318-0.0815-0.18670.17610.03360.11560.02320.0980.0292-0.07280.0736-0.08710.0026-0.01010.03770.1473-0.0096-0.01350.12850.01790.1251-5.9139-25.7375-36.2382
40.02220.00990.01350.00490.00670.01380.055-0.056-0.04050.2977-0.093-0.3667-0.33220.290700.3201-0.05-0.00560.1722-0.01980.3331-1.1731-6.7671-16.9155
50.32530.2141-0.09960.6270.09760.10710.02070.00670.0713-0.0079-0.01210.10340.0012-0.03880.00060.113-0.00070.00130.10980.00330.1084-8.1859-29.3346-24.9309
60.2401-0.2288-0.21270.42190.00410.398-0.0179-0.18430.13890.1320.00040.1194-0.0836-0.0603-0.07850.17550.01960.04250.1923-0.02730.1649-16.23-23.9555-6.7202
70.4508-0.11690.05540.2119-0.22840.34030.0423-0.1321-0.27910.16730.04880.09590.07020.07750.05330.16590.00130.0530.2271-0.01170.1252-15.0243-32.9414-2.1452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 37 )A0 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 112 )A38 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 143 )A113 - 143
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 7 )B0 - 7
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 66 )B8 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 112 )B67 - 112
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 142 )B113 - 142

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