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- PDB-7ppt: Structure of diFe-Sulerythrin at 0.26 MGy total absorbed dose -

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Basic information

Entry
Database: PDB / ID: 7ppt
TitleStructure of diFe-Sulerythrin at 0.26 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: 1.42 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)32,78911
Polymers32,3382
Non-polymers4509
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-140 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.032, 72.032, 98.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
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...A0 - 601
151(chain A and (resid 3 through 4 or resid 6...A109 - 119
161(chain A and (resid 3 through 4 or resid 6...A0 - 601
171(chain A and (resid 3 through 4 or resid 6...A136 - 142
181(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...B9 - 21
241(chain B and (resid 3 through 4 or resid 6...B0 - 601
251(chain B and (resid 3 through 4 or resid 6...B109 - 119
261(chain B and (resid 3 through 4 or resid 6...B0 - 601
271(chain B and (resid 3 through 4 or resid 6...B129 - 134
281(chain B and (resid 3 through 4 or resid 6...B136 - 601

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 327 molecules

#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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 45.93 %
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: 1.42→38.545 Å / Num. obs: 107347 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.92 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.041 / Rrim(I) all: 0.143 / Net I/σ(I): 7.3
Reflection shellResolution: 1.42→1.51 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 17278 / CC1/2: 0.64 / Rpim(I) all: 0.303 / Rrim(I) all: 0.974 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXV1.13-2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J30

1j30


Resolution: 1.42→38.545 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2104 1.96 %
Rwork0.185 105224 -
obs0.1855 107328 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.75 Å2 / Biso mean: 22.8175 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: final / Resolution: 1.42→38.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 30 318 2606
Biso mean--20.88 33.56 -
Num. residues----287
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1162X-RAY DIFFRACTION6.974TORSIONAL
12B1162X-RAY DIFFRACTION6.974TORSIONAL
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)
13.2784-0.6694-0.45634.48940.5992.17120.0605-0.10590.29360.05080.0187-0.4689-0.350.1257-0.05640.26630.065-0.0410.3498-0.07360.403233.944932.4897-21.1663
21.0025-0.022-0.22510.6390.1240.7309-0.0006-0.0863-0.06820.05140.0164-0.1150.00680.0411-0.0040.14370.0037-0.02310.12640.0090.136213.281630.513-20.5289
30.60220.14460.09291.2068-0.00840.2064-0.00720.039-0.1286-0.1330.0432-0.06620.01610.0463-0.02570.1561-0.00770.01250.1452-0.02150.15325.848420.7562-34.3666
46.2346-0.3004-1.56263.27740.49623.1287-0.07310.0067-0.4970.6718-0.08330.2240.6709-0.23470.13120.3944-0.0486-0.05460.1750.04350.37093.19596.3487-18.803
50.71720.02150.07960.9187-0.11920.47550.0012-0.0877-0.11480.06310.013-0.11190.05550.0409-0.00550.12590.0071-0.0130.13660.00380.120711.828227.5005-18.0787
60.8051-0.22110.44260.87380.14411.2158-0.0808-0.2322-0.05980.21410.0399-0.11940.0586-0.14850.00840.1971-0.0022-0.04570.24290.01790.138314.239532.7312-3.6084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 7 )A0 - 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 0 through 7 )B0 - 7
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 112 )B8 - 112
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 141 )B113 - 141

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