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- PDB-8e7y: RsTSPO A138F with two heme bound -

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Basic information

Entry
Database: PDB / ID: 8e7y
TitleRsTSPO A138F with two heme bound
ComponentsTryptophan-rich sensory protein
KeywordsMEMBRANE PROTEIN / Translocator Protein 18 kD / TSPO
Function / homology
Function and homology information


tetrapyrrole metabolic process / tetrapyrrole binding / lipid binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
TspO/MBR-related protein / TspO/MBR-related superfamily / TspO/MBR family
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Tryptophan-rich sensory protein
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, J. / Hiser, C. / Li, F. / Garavito, R. / Ferguson-Miller, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2023
Title: New TSPO Crystal Structures of Mutant and Heme-Bound Forms with Altered Flexibility, Ligand Binding, and Porphyrin Degradation Activity.
Authors: Liu, J. / Hiser, C. / Li, F. / Hall, R. / Garavito, R.M. / Ferguson-Miller, S.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: 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
B: Tryptophan-rich sensory protein
A: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,49410
Polymers36,1222
Non-polymers3,3728
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-76 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 95.350, 105.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 25 or (resid 26...
21(chain B and (resid 1 through 152 or (resid 153...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 25 or (resid 26...A1 - 25
121(chain A and (resid 1 through 25 or (resid 26...A26
131(chain A and (resid 1 through 25 or (resid 26...A1 - 157
141(chain A and (resid 1 through 25 or (resid 26...A1 - 157
151(chain A and (resid 1 through 25 or (resid 26...A1 - 157
161(chain A and (resid 1 through 25 or (resid 26...A1 - 157
211(chain B and (resid 1 through 152 or (resid 153...B1 - 152
221(chain B and (resid 1 through 152 or (resid 153...B153
231(chain B and (resid 1 through 152 or (resid 153...B1 - 157
241(chain B and (resid 1 through 152 or (resid 153...B1 - 157
251(chain B and (resid 1 through 152 or (resid 153...B1 - 157
261(chain B and (resid 1 through 152 or (resid 153...B1 - 157
112chain CC - A205
212chain DD - B203

NCS ensembles :
ID
1
2

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Components

#1: Protein Tryptophan-rich sensory protein / TSPO / Translocator protein TspO / TspO regulatory protein


Mass: 18061.137 Da / Num. of mol.: 2 / Mutation: A138F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: tspO, crtK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RFC8
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 28-32% PEG 400, 300mM ammonium formate, 100mM Tris (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→47.69 Å / Num. obs: 18728 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.43 / Num. unique obs: 1832 / CC1/2: 0.698 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UC1

4uc1


Resolution: 2.3→46.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 560 3 %
Rwork0.2157 18107 -
obs0.2167 18667 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 55.4784 Å2 / Biso min: 36.29 Å2
Refinement stepCycle: final / Resolution: 2.3→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 194 10 2716
Biso mean--66.4 53.18 -
Num. residues----314
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A998X-RAY DIFFRACTION12.013TORSIONAL
12B998X-RAY DIFFRACTION12.013TORSIONAL
21A16X-RAY DIFFRACTION12.013TORSIONAL
22B16X-RAY DIFFRACTION12.013TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.530.32571380.230644454583
2.53-2.90.27321380.222444734611
2.9-3.650.27511390.226845054644
3.65-46.170.22661450.207846844829

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