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- PDB-8e7z: RsTSPO mutant -A138F -

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Basic information

Entry
Database: PDB / ID: 8e7z
TitleRsTSPO mutant -A138F
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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Tryptophan-rich sensory protein
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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
A: Tryptophan-rich sensory protein
B: Tryptophan-rich sensory protein
C: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,28118
Polymers54,1833
Non-polymers5,09815
Water81145
1
A: Tryptophan-rich sensory protein
B: Tryptophan-rich sensory protein
hetero molecules

A: Tryptophan-rich sensory protein
B: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,37524
Polymers72,2454
Non-polymers7,13120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area7070 Å2
ΔGint-74 kcal/mol
Surface area28290 Å2
MethodPISA
2
C: Tryptophan-rich sensory protein
hetero molecules

C: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,18712
Polymers36,1222
Non-polymers3,06510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3880 Å2
ΔGint-28 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.553, 99.535, 95.484
Angle α, β, γ (deg.)90.000, 100.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-313-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 27 or (resid 28...
21(chain B and (resid 3 through 32 or (resid 33...
31(chain C and (resid 3 through 42 or (resid 43...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 27 or (resid 28...A3 - 27
121(chain A and (resid 3 through 27 or (resid 28...A28 - 29
131(chain A and (resid 3 through 27 or (resid 28...A1 - 156
141(chain A and (resid 3 through 27 or (resid 28...A1 - 156
151(chain A and (resid 3 through 27 or (resid 28...A1 - 156
161(chain A and (resid 3 through 27 or (resid 28...A1 - 156
211(chain B and (resid 3 through 32 or (resid 33...B3 - 32
221(chain B and (resid 3 through 32 or (resid 33...B33
231(chain B and (resid 3 through 32 or (resid 33...B3 - 157
241(chain B and (resid 3 through 32 or (resid 33...B3 - 157
251(chain B and (resid 3 through 32 or (resid 33...B3 - 157
261(chain B and (resid 3 through 32 or (resid 33...B3 - 157
311(chain C and (resid 3 through 42 or (resid 43...C3 - 42
321(chain C and (resid 3 through 42 or (resid 43...C43
331(chain C and (resid 3 through 42 or (resid 43...C2 - 150
341(chain C and (resid 3 through 42 or (resid 43...C2 - 150
351(chain C and (resid 3 through 42 or (resid 43...C2 - 150
361(chain C and (resid 3 through 42 or (resid 43...C0
371(chain C and (resid 3 through 42 or (resid 43...C2 - 150
381(chain C and (resid 3 through 42 or (resid 43...C2 - 150
391(chain C and (resid 3 through 42 or (resid 43...C2 - 150
3101(chain C and (resid 3 through 42 or (resid 43...C2 - 150
3111(chain C and (resid 3 through 42 or (resid 43...C2 - 150

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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.: 3 / 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.: 14 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 26-30% PEG600, HEPES pH 7.5, 100mM Sodium Acetate, 100mM Zinc Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→47.14 Å / Num. obs: 16650 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.371 / Num. unique obs: 1658 / CC1/2: 0.615

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4uc1


Resolution: 2.6→47.13 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 833 5.01 %
Rwork0.2036 15801 -
obs0.2065 16634 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.68 Å2 / Biso mean: 34.5347 Å2 / Biso min: 13.55 Å2
Refinement stepCycle: final / Resolution: 2.6→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 297 45 3981
Biso mean--45.28 36.52 -
Num. residues----459
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1329X-RAY DIFFRACTION6.274TORSIONAL
12B1329X-RAY DIFFRACTION6.274TORSIONAL
13C1329X-RAY DIFFRACTION6.274TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.760.29251390.223226392778
2.76-2.980.27791370.216626002737
2.98-3.280.27821380.216926202758
3.28-3.750.24561390.204526212760
3.75-4.720.27861390.189926392778
4.72-47.130.23251410.197626822823

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