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- PDB-8e7w: RsTSPO A139T with Heme -

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Basic information

Entry
Database: PDB / ID: 8e7w
TitleRsTSPO A139T with Heme
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 / Chem-P6L / Tryptophan-rich sensory protein
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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)61,11321
Polymers54,0453
Non-polymers7,06818
Water2,126118
1
A: Tryptophan-rich sensory protein
B: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,67216
Polymers36,0302
Non-polymers5,64214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-53 kcal/mol
Surface area15340 Å2
MethodPISA
2
C: Tryptophan-rich sensory protein
hetero molecules

C: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,88210
Polymers36,0302
Non-polymers2,8528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4130 Å2
ΔGint-46 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.399, 99.568, 95.812
Angle α, β, γ (deg.)90.000, 100.160, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 23 or (resid 24...
21(chain B and (resid 3 through 23 or (resid 24...
31(chain C and (resid 3 through 32 or (resid 33...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 3 through 23 or (resid 24...AA3 - 233 - 23
12LEULEULEULEU(chain A and (resid 3 through 23 or (resid 24...AA2424
13METMETARGARG(chain A and (resid 3 through 23 or (resid 24...AA1 - 1571 - 157
14METMETARGARG(chain A and (resid 3 through 23 or (resid 24...AA1 - 1571 - 157
15METMETARGARG(chain A and (resid 3 through 23 or (resid 24...AA1 - 1571 - 157
16METMETARGARG(chain A and (resid 3 through 23 or (resid 24...AA1 - 1571 - 157
21METMETALAALA(chain B and (resid 3 through 23 or (resid 24...BB3 - 233 - 23
22LEULEULEULEU(chain B and (resid 3 through 23 or (resid 24...BB2424
23ASNASNARGARG(chain B and (resid 3 through 23 or (resid 24...BB2 - 1572 - 157
24ASNASNARGARG(chain B and (resid 3 through 23 or (resid 24...BB2 - 1572 - 157
25ASNASNARGARG(chain B and (resid 3 through 23 or (resid 24...BB2 - 1572 - 157
26ASNASNARGARG(chain B and (resid 3 through 23 or (resid 24...BB2 - 1572 - 157
31METMETASPASP(chain C and (resid 3 through 32 or (resid 33...CC3 - 323 - 32
32ASNASNASNASN(chain C and (resid 3 through 32 or (resid 33...CC3333
33ASNASNASNASN(chain C and (resid 3 through 32 or (resid 33...CC2 - 1502 - 150
34ASNASNASNASN(chain C and (resid 3 through 32 or (resid 33...CC2 - 1502 - 150
35ASNASNASNASN(chain C and (resid 3 through 32 or (resid 33...CC2 - 1502 - 150
36ASNASNASNASN(chain C and (resid 3 through 32 or (resid 33...CC2 - 1502 - 150

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Components

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


Mass: 18015.066 Da / Num. of mol.: 3 / Mutation: A139T
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.: 16 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 28-30% PEG400, HEPES (pH 8.5), 100mM sodium acetate, 100 mM ammonium acetate

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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 PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→28.95 Å / Num. obs: 31427 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2 / Num. unique obs: 3098 / CC1/2: 0.583 / % possible all: 99

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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: 2.1→28.95 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 949 3.02 %
Rwork0.1951 30433 -
obs0.1968 31382 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.6 Å2 / Biso mean: 34.9326 Å2 / Biso min: 15.54 Å2
Refinement stepCycle: final / Resolution: 2.1→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 394 118 4178
Biso mean--52.13 42.63 -
Num. residues----462
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1329X-RAY DIFFRACTION8.917TORSIONAL
12B1329X-RAY DIFFRACTION8.917TORSIONAL
13C1329X-RAY DIFFRACTION8.917TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.210.31791350.25174284441999
2.21-2.350.27261420.2284300444299
2.35-2.530.26861360.209443724508100
2.53-2.780.24681500.195243104460100
2.78-3.190.24391370.188843574494100
3.19-4.010.25211320.18543744506100
4.01-28.950.23681170.18444364553100

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