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- PDB-4uc3: Translocator protein 18 kDa (TSPO) from Rhodobacter sphaeroides w... -

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Basic information

Entry
Database: PDB / ID: 4uc3
TitleTranslocator protein 18 kDa (TSPO) from Rhodobacter sphaeroides wild type
ComponentsTRANSLOCATOR PROTEIN TSPO
KeywordsMEMBRANE PROTEIN / mitochondria / transport / transmembrane protein
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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-YZY / Tryptophan-rich sensory protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)37,0026
Polymers35,3372
Non-polymers1,6654
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-31 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.100, 61.706, 52.676
Angle α, β, γ (deg.)90.000, 112.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGchain AAA3 - 1571 - 155
2ALAALAchain BBB3 - 1461 - 144

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Components

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


Mass: 17668.664 Da / Num. of mol.: 2
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.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-YZY / (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate


Mass: 594.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H70O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 32% (w/v) PEG 1000, 100 mM Zn(CH3CO2)2, 100 mM MES, 100 mM NaCH3CO2, K or NH4CH3CO2, and 6-8 % (v/v) 2-propanol

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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: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.5→45.35 Å / Num. obs: 9874 / % possible obs: 97.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.226 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata scaling
Aimlessdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.209 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 372 3.77 %Random selection
Rwork0.2179 ---
obs0.2202 9873 97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.31 Å2 / Biso mean: 35.2583 Å2 / Biso min: 17.3 Å2
Refinement stepCycle: final / Resolution: 2.5→42.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 104 10 2276
Biso mean--40.59 34.78 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012339
X-RAY DIFFRACTIONf_angle_d1.3933170
X-RAY DIFFRACTIONf_chiral_restr0.048345
X-RAY DIFFRACTIONf_plane_restr0.006369
X-RAY DIFFRACTIONf_dihedral_angle_d19.531815
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1100X-RAY DIFFRACTION6.413TORSIONAL
12B1100X-RAY DIFFRACTION6.413TORSIONAL

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