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- PDB-4ryj: Crystal structure of apo dimer of BcTSPO -

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Basic information

Entry
Database: PDB / ID: 4ryj
TitleCrystal structure of apo dimer of BcTSPO
ComponentsIntegral membrane protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / Receptor
Function / homologyTspO/MBR-related protein / TspO/MBR-related superfamily / TspO/MBR family / tetrapyrrole metabolic process / tetrapyrrole binding / identical protein binding / membrane / plasma membrane / Tryptophan-rich protein TspO
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsGuo, Y. / Liu, Q. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Science / Year: 2015
Title: Protein structure. Structure and activity of tryptophan-rich TSPO proteins.
Authors: Guo, Y. / Kalathur, R.C. / Liu, Q. / Kloss, B. / Bruni, R. / Ginter, C. / Kloppmann, E. / Rost, B. / Hendrickson, W.A.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integral membrane protein
B: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)42,9942
Polymers42,9942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-59 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.980, 104.930, 53.860
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integral membrane protein


Mass: 21496.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: DSM 31 / Gene: BC_3136 / Plasmid: pMCSG7 10xHis 30021246 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81BL7

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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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.2
Details: A sitting drop containing 2 L of BcTSPO (10mg/mL) was mixed with 2 uL of solution A (0.15 M sodium formate, 0.1 M HEPES pH7.2, 18 % w/v PEG 3350) and placed over a well containing 80 uL of 0. ...Details: A sitting drop containing 2 L of BcTSPO (10mg/mL) was mixed with 2 uL of solution A (0.15 M sodium formate, 0.1 M HEPES pH7.2, 18 % w/v PEG 3350) and placed over a well containing 80 uL of 0.1 M HEPES pH7.2, 18 % w/v PEG 3350 and 20 uL of solution A, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2014
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 4.1→38 Å / Num. all: 10424 / Num. obs: 5345 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Net I/σ(I): 1.63
Reflection shellResolution: 4.1→4.21 Å / % possible all: 91.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→36.951 Å / SU ML: 0.89 / σ(F): 1.34 / Phase error: 45.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3736 141 4.92 %
Rwork0.3451 --
obs0.3466 2868 99.03 %
all-2868 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→36.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 0 0 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052536
X-RAY DIFFRACTIONf_angle_d1.0683482
X-RAY DIFFRACTIONf_dihedral_angle_d11.616808
X-RAY DIFFRACTIONf_chiral_restr0.043398
X-RAY DIFFRACTIONf_plane_restr0.005408
LS refinement shellResolution: 4.1001→36.9528 Å
RfactorNum. reflection% reflection
Rfree0.3736 141 -
Rwork0.3451 2727 -
obs--99 %

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