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- PDB-4rym: Crystal structure of BcTSPO Iodo Type1 monomer -

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Basic information

Entry
Database: PDB / ID: 4rym
TitleCrystal structure of BcTSPO Iodo Type1 monomer
ComponentsIntegral membrane protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / Receptor
Function / homology
Function and homology information


tetrapyrrole metabolic process / tetrapyrrole 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
IODIDE ION / Tryptophan-rich protein TspO
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8784
Polymers21,4971
Non-polymers3813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.356, 49.538, 99.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Integral membrane protein


Mass: 21496.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_3136, DSM 31 / Plasmid: pMCSG7 10xHis 30021246 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81BL7
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 293 K / Method: lcp / pH: 6.5
Details: crystals grew from 0.1 M sodium cacodylate, 5% w/v PGA LM (poly-l-glutamic acid, low molecular weight~ 200-400 kDa), 30% v/v PEG 550MME (Polyethylene glycol monomethyl ether 550), pH 6.5 in ...Details: crystals grew from 0.1 M sodium cacodylate, 5% w/v PGA LM (poly-l-glutamic acid, low molecular weight~ 200-400 kDa), 30% v/v PEG 550MME (Polyethylene glycol monomethyl ether 550), pH 6.5 in LCP with monoolein (9.9 MAG), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 2.0735 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2014
RadiationMonochromator: A KOHZU double crystal monochromator with a sagittally focused second crystal.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0735 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 4153 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.87 Å / % possible all: 70.5

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Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→35.053 Å / SU ML: 0.34 / σ(F): 1.39 / Phase error: 30.67 / Stereochemistry target values: ML / Details: Multi-Crystal Iodine SAD
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 194 4.71 %Random
Rwork0.2174 ---
obs0.2196 4122 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→35.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 3 0 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051303
X-RAY DIFFRACTIONf_angle_d0.7681784
X-RAY DIFFRACTIONf_dihedral_angle_d11.51422
X-RAY DIFFRACTIONf_chiral_restr0.03202
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shellResolution: 2.8→35.0556 Å
RfactorNum. reflection% reflection
Rfree0.2718 194 -
Rwork0.2174 3928 -
obs--94 %

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