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- PDB-5duo: Crystal structure of native translocator protein 18kDa (TSPO) fro... -

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Basic information

Entry
Database: PDB / ID: 5duo
TitleCrystal structure of native translocator protein 18kDa (TSPO) from Rhodobacter sphaeroides (A139T Mutant) in C2 space group
ComponentsTryptophan-rich sensory protein
KeywordsMEMBRANE PROTEIN / mitochondria / transport / 5 transmembrane helices
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
FORMIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PROTOPORPHYRIN IX / Tryptophan-rich sensory protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, F. / Liu, J. / Zheng, Y. / Garavito, R.M. / Ferguson-Miller, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM26916 United States
CitationJournal: Science / Year: 2015
Title: Response to Comment on "Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism".
Authors: Li, F. / Liu, J. / Zheng, Y. / Garavito, R.M. / Ferguson-Miller, S.
History
DepositionSep 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)59,83521
Polymers53,8323
Non-polymers6,00318
Water1,09961
1
A: Tryptophan-rich sensory protein
B: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,46516
Polymers35,8882
Non-polymers4,57714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-45 kcal/mol
Surface area15640 Å2
MethodPISA
2
C: Tryptophan-rich sensory protein
hetero molecules

C: Tryptophan-rich sensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,74010
Polymers35,8882
Non-polymers2,8528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3660 Å2
ΔGint-34 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.388, 99.191, 95.326
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-312-

HOH

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Components

#1: Protein Tryptophan-rich sensory protein / TSPO / Translocator protein TspO / TspO regulatory protein / Translocator protein 18 kDa


Mass: 17943.988 Da / Num. of mol.: 3 / Mutation: A139T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter 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.: 15 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PP9 / PROTOPORPHYRIN IX


Mass: 562.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34N4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsProtoporphyrin IX was used as a representative of a porphyrin compound and was the best ...Protoporphyrin IX was used as a representative of a porphyrin compound and was the best interpretation of the extra density based on spectral data that showed what appeared to be an oxidized porphyrin.

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 31% v/v pentaerythritol ethoxylate 15/04, 100 mM Tris, pH 7.0, 200 mM ammonium acetate
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.003 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 4, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.4→47 Å / Num. all: 22331 / Num. obs: 22331 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1402 / Net I/σ(I): 8.68
Reflection shellResolution: 2.349→2.433 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.127 / Mean I/σ(I) obs: 1.15 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.984 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 837 4.01 %Random selection
Rwork0.1889 20059 --
obs0.1912 20896 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.11 Å2 / Biso mean: 42.3742 Å2 / Biso min: 19.49 Å2
Refinement stepCycle: final / Resolution: 2.4→46.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 391 61 4183
Biso mean--54.36 44.04 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094255
X-RAY DIFFRACTIONf_angle_d1.1515730
X-RAY DIFFRACTIONf_chiral_restr0.046585
X-RAY DIFFRACTIONf_plane_restr0.006652
X-RAY DIFFRACTIONf_dihedral_angle_d16.6322435
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.55040.37071390.277433073446
2.5504-2.74730.30341390.223233363475
2.7473-3.02370.2781390.207333463485
3.0237-3.46110.26431390.181433233462
3.4611-4.36020.19731400.162933483488
4.3602-46.99340.22011410.177733993540

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