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- PDB-8e7x: RsTSPO A138F with one Heme bound -

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Basic information

Entry
Database: PDB / ID: 8e7x
TitleRsTSPO A138F with one 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 / membrane / identical protein binding / 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 / 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)58,00913
Polymers54,1833
Non-polymers3,82510
Water97354
1
A: Tryptophan-rich sensory protein
B: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,23510
Polymers36,1222
Non-polymers3,1128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-55 kcal/mol
Surface area14130 Å2
MethodPISA
2
C: Tryptophan-rich sensory protein
hetero molecules

C: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5486
Polymers36,1222
Non-polymers1,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3240 Å2
ΔGint-35 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.952, 100.103, 95.614
Angle α, β, γ (deg.)90.000, 100.230, 90.000
Int Tables number5
Space group name H-MC121
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 25 or (resid 26...
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
11METMETPROPRO(chain A and (resid 3 through 27 or (resid 28...AA3 - 273 - 27
12ASPASPGLUGLU(chain A and (resid 3 through 27 or (resid 28...AA28 - 2928 - 29
13METMETARGARG(chain A and (resid 3 through 27 or (resid 28...AA1 - 1571 - 157
14METMETARGARG(chain A and (resid 3 through 27 or (resid 28...AA1 - 1571 - 157
15METMETARGARG(chain A and (resid 3 through 27 or (resid 28...AA1 - 1571 - 157
16METMETARGARG(chain A and (resid 3 through 27 or (resid 28...AA1 - 1571 - 157
21METMETLEULEU(chain B and (resid 3 through 25 or (resid 26...BB3 - 253 - 25
22LYSLYSLYSLYS(chain B and (resid 3 through 25 or (resid 26...BB2626
23ASNASNARGARG(chain B and (resid 3 through 25 or (resid 26...BB2 - 1572 - 157
24ASNASNARGARG(chain B and (resid 3 through 25 or (resid 26...BB2 - 1572 - 157
25ASNASNARGARG(chain B and (resid 3 through 25 or (resid 26...BB2 - 1572 - 157
26ASNASNARGARG(chain B and (resid 3 through 25 or (resid 26...BB2 - 1572 - 157
31METMETASPASP(chain C and (resid 3 through 32 or (resid 33...CC3 - 323 - 32
32ASNASNLEULEU(chain C and (resid 3 through 32 or (resid 33...CC33 - 3433 - 34
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: 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.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 28-30% PEG1000, 50mM Sodium Chloride, 20mM Glycine (pH 9.0), 6% 2-Propanol

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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 EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→44.2 Å / Num. obs: 30027 / % possible obs: 99 % / Redundancy: 1.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Net I/σ(I): 4.9
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3066 / CC1/2: 0.654

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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: 2.1→44.19 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1487 4.96 %
Rwork0.1961 28515 -
obs0.1979 30002 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.48 Å2 / Biso mean: 30.7942 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 2.1→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 225 54 3925
Biso mean--43.97 32.78 -
Num. residues----462
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1332X-RAY DIFFRACTION8.336TORSIONAL
12B1332X-RAY DIFFRACTION8.336TORSIONAL
13C1332X-RAY DIFFRACTION8.336TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.170.28561220.24982646276898
2.17-2.250.27821400.22322671281199
2.25-2.340.28231440.21552641278598
2.34-2.440.23671360.20212618275497
2.44-2.570.2361490.18822575272496
2.57-2.730.22031220.18572646276897
2.73-2.940.24111510.18512579273096
2.94-3.240.25551300.19762568269895
3.24-3.710.23041350.18942556269195
3.71-4.670.21851210.18932548266993
4.67-44.190.21370.1922467260490

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