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- PDB-4uc1: High resolution crystal structure of translocator protein 18kDa (... -

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Basic information

Entry
Database: PDB / ID: 4uc1
TitleHigh resolution crystal structure of translocator protein 18kDa (TSPO) from Rhodobacter sphaeroides (A139T Mutant) in C2 space group
ComponentsTranslocator protein TspO
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
METHOXY-ETHOXYL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / PROTOPORPHYRIN IX / Chem-Z0P / Tryptophan-rich sensory protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / MAD / molecular replacement / Resolution: 1.8 Å
AuthorsLi, F. / Liu, J. / Zheng, Y. / Garavito, R.M. / Ferguson-Miller, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM26916 United States
Michigan State University Strategic Partnership Grant, Mitochondrial Science & Medicine 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: Database references / Structure summary
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
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 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Translocator protein TspO
B: Translocator protein TspO
C: Translocator protein TspO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,45024
Polymers53,8323
Non-polymers7,61821
Water1,49583
1
A: Translocator protein TspO
B: Translocator protein TspO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,68117
Polymers35,8882
Non-polymers5,79315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-32 kcal/mol
Surface area15950 Å2
MethodPISA
2
C: Translocator protein TspO
hetero molecules

C: Translocator protein TspO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,53914
Polymers35,8882
Non-polymers3,65112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3380 Å2
ΔGint-33 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.632, 99.544, 95.210
Angle α, β, γ (deg.)90.000, 99.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 17943.988 Da / Num. of mol.: 3 / 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

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Non-polymers , 6 types, 104 molecules

#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-PP9 / PROTOPORPHYRIN IX


Mass: 562.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34N4O4
#4: Chemical ChemComp-Z0P / (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate


Mass: 594.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H70O5
#5: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#6: Chemical ChemComp-MOE / METHOXY-ETHOXYL


Mass: 75.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 32% PEG 400, 0.05 M NaCl, 0.04 M MgCl2 and 0.1 M HEPES buffer

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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: 1.8→43.97 Å / Num. obs: 97994 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.41 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1 / % possible all: 99.9

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Blu-Icedata collection
XDSdata scaling
XSCALEdata scaling
SHARP2.8.2phasing
PHASERphasing
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MIR / Resolution: 1.8→43.965 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 --Random selection
Rwork0.2009 94954 --
obs0.2023 97994 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.88 Å2 / Biso mean: 33.937 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.8→43.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 489 83 4295
Biso mean--51.1 39.82 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014379
X-RAY DIFFRACTIONf_angle_d1.1555875
X-RAY DIFFRACTIONf_chiral_restr0.046591
X-RAY DIFFRACTIONf_plane_restr0.006662
X-RAY DIFFRACTIONf_dihedral_angle_d18.71646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82810.40951340.38924207X-RAY DIFFRACTION99
1.8281-1.85810.37921400.36714367X-RAY DIFFRACTION99
1.8581-1.89010.32171370.35574283X-RAY DIFFRACTION99
1.8901-1.92450.35331400.3234323X-RAY DIFFRACTION99
1.9245-1.96150.30561370.30834240X-RAY DIFFRACTION100
1.9615-2.00160.32571390.28244401X-RAY DIFFRACTION100
2.0016-2.04510.29431380.26044275X-RAY DIFFRACTION100
2.0451-2.09270.27561370.24744326X-RAY DIFFRACTION100
2.0927-2.1450.28371400.23474366X-RAY DIFFRACTION100
2.145-2.2030.25231360.22374283X-RAY DIFFRACTION100
2.203-2.26780.27471420.20584329X-RAY DIFFRACTION100
2.2678-2.3410.24431380.19714330X-RAY DIFFRACTION100
2.341-2.42470.20911360.18574329X-RAY DIFFRACTION100
2.4247-2.52170.23561380.17984329X-RAY DIFFRACTION100
2.5217-2.63650.20821380.17444314X-RAY DIFFRACTION100
2.6365-2.77550.24071380.17584307X-RAY DIFFRACTION100
2.7755-2.94930.24781400.17814330X-RAY DIFFRACTION100
2.9493-3.1770.2331380.18824329X-RAY DIFFRACTION100
3.177-3.49660.23471350.1854300X-RAY DIFFRACTION100
3.4966-4.00220.21111400.17384359X-RAY DIFFRACTION100
4.0022-5.04120.23651420.16914300X-RAY DIFFRACTION100
5.0412-43.97770.22591370.18764327X-RAY DIFFRACTION99

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