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- PDB-4ryr: Crystal structure of BcTSPO, type 2 at 1.7 Angstrom with DMSO -

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Basic information

Entry
Database: PDB / ID: 4ryr
TitleCrystal structure of BcTSPO, type 2 at 1.7 Angstrom with DMSO
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
Chem-MPG / Tryptophan-rich protein TspO
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 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 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jun 15, 2016Group: Non-polymer description
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)25,01814
Polymers21,4971
Non-polymers3,52113
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.906, 54.658, 107.579
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: DSM 31 / Gene: BC_3136 / Plasmid: pMCSG7 10xHis 30021246 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81BL7
#2: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 293 K / Method: lcp / pH: 5.5
Details: crystals grew from 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3,350 in LCP, 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: May 10, 2014
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 32904 / Num. obs: 18066 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.73 Å / % possible all: 59.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RYM

4rym


Resolution: 1.704→38.338 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 876 4.86 %Random
Rwork0.1918 ---
obs0.193 18010 92.95 %-
all-18066 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.704→38.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 144 74 1440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111399
X-RAY DIFFRACTIONf_angle_d1.4051873
X-RAY DIFFRACTIONf_dihedral_angle_d15.12477
X-RAY DIFFRACTIONf_chiral_restr0.052204
X-RAY DIFFRACTIONf_plane_restr0.006212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.704-1.81050.34751120.30092261X-RAY DIFFRACTION75
1.8105-1.95030.29041400.24012846X-RAY DIFFRACTION94
1.9503-2.14650.20251430.1812896X-RAY DIFFRACTION96
2.1465-2.45710.19351540.15132892X-RAY DIFFRACTION95
2.4571-3.09550.18941670.1772998X-RAY DIFFRACTION97
3.0955-38.3480.21681600.19713241X-RAY DIFFRACTION100

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