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- PDB-4ryi: Crystal structure of BcTSPO/PK11195 complex -

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Basic information

Entry
Database: PDB / ID: 4ryi
TitleCrystal structure of BcTSPO/PK11195 complex
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-PKA / Tryptophan-rich protein TspO
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7004
Polymers42,9942
Non-polymers7062
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-20 kcal/mol
Surface area14940 Å2
MethodPISA
2
A: Integral membrane protein
hetero molecules

B: Integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7004
Polymers42,9942
Non-polymers7062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area1250 Å2
ΔGint-16 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.666, 54.550, 58.560
Angle α, β, γ (deg.)90.00, 105.70, 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: 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-PKA / N-[(2R)-butan-2-yl]-1-(2-chlorophenyl)-N-methylisoquinoline-3-carboxamide


Mass: 352.857 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21ClN2O

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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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 3% PEG 4000, 0.066 sodium chloride, 0.02 Tris,pH 7.5 as crystallization buffer, covered the drop of a mix of (10mg/mL protein and saturated PK11195 in 8% DMSO):monoolein in a ratio of 2/3 ...Details: 3% PEG 4000, 0.066 sodium chloride, 0.02 Tris,pH 7.5 as crystallization buffer, covered the drop of a mix of (10mg/mL protein and saturated PK11195 in 8% DMSO):monoolein in a ratio of 2/3 (v/v), 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: Jun 21, 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: 3.49→50 Å / Num. obs: 4245 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 4.35
Reflection shellResolution: 3.5→3.56 Å / % possible all: 88.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CaspRmodel building
PHENIX(phenix.refine: 1.9_1690)refinement
HKL-2000data reduction
HKL-2000data scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→35.12 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 36.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3137 195 4.62 %Random
Rwork0.2359 ---
obs0.2397 4221 93.9 %-
all-4245 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 50 0 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052644
X-RAY DIFFRACTIONf_angle_d0.8983618
X-RAY DIFFRACTIONf_dihedral_angle_d13.535862
X-RAY DIFFRACTIONf_chiral_restr0.034402
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shellResolution: 3.49→35.1214 Å
RfactorNum. reflection% reflection
Rfree0.3137 195 -
Rwork0.2359 4026 -
obs--94 %

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