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- PDB-4uc2: Crystal structure of translocator protein 18kDa (TSPO) from rhodo... -

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Basic information

Entry
Database: PDB / ID: 4uc2
TitleCrystal structure of translocator protein 18kDa (TSPO) from rhodobacter sphaeroides (A139T mutant) in P212121 space group
ComponentsTRANSLOCATOR PROTEIN TSPO
KeywordsMEMBRANE PROTEIN / mitochondria / transport / transmembrane protein
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 / 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)NIH GM26916 United States
CitationJournal: Science / Year: 2015
Title: 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
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Structure summary
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSLOCATOR PROTEIN TSPO
B: TRANSLOCATOR PROTEIN TSPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9599
Polymers35,6262
Non-polymers2,3337
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-29 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.083, 95.837, 105.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSLOCATOR PROTEIN TSPO / TRYPTOPHAN-RICH SENSORY PROTEIN


Mass: 17812.791 Da / Num. of mol.: 2 / Mutation: A139T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / 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
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.5
Details: 23% PEG 3350, 0.1 M (NH4)2SO4 and 0.1 M Hepes buffer pH 8.5

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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: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.4→43.65 Å / Num. obs: 29986 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.36 Å2 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UC1

4uc1


Resolution: 2.4→43.65 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1203 4.01 %Random selection
Rwork0.2056 28783 --
obs0.2069 29986 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.81 Å2 / Biso mean: 42.4165 Å2 / Biso min: 16.06 Å2
Refinement stepCycle: final / Resolution: 2.4→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 137 35 2684
Biso mean--53.73 47.32 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092740
X-RAY DIFFRACTIONf_angle_d1.1183718
X-RAY DIFFRACTIONf_chiral_restr0.039389
X-RAY DIFFRACTIONf_plane_restr0.006436
X-RAY DIFFRACTIONf_dihedral_angle_d17.59958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.49620.33511340.298431893323100
2.4962-2.60970.31381350.269332123347100
2.6097-2.74730.28541270.231732283355100
2.7473-2.91940.25561290.205231863315100
2.9194-3.14480.20161370.202231983335100
3.1448-3.46110.22871340.190331933327100
3.4611-3.96170.24071280.2053198332699
3.9617-4.99010.23041380.189231953333100
4.9901-43.65920.20481410.19131843325100

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