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- PDB-5vh0: RHCC in complex with pyrene -

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Basic information

Entry
Database: PDB / ID: 5vh0
TitleRHCC in complex with pyrene
ComponentsTetrabrachion
KeywordsTRANSPORT PROTEIN / nanotube / Polycyclic aromatic hydrocarbons / passive sample device / surface layer
Function / homology
Function and homology information


Tetrabrachion / Tetrabrachion / Tetrabrachion, parallel right-handed coiled coil domain / Tetrabrachion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
pyrene / Tetrabrachion
Similarity search - Component
Biological speciesStaphylothermus marinus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.055 Å
AuthorsMcDougall, M. / Francisco, O. / Stetefeld, J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council of Canada- Discovery GrantRGPIN-342077-2012 Canada
Natural Sciences and Engineering Research Council of Canada- Strategic Partnership GrantSTGP-479210-2015 Canada
CitationJournal: Sci Rep / Year: 2019
Title: Proteinaceous Nano container Encapsulate Polycyclic Aromatic Hydrocarbons.
Authors: McDougall, M. / Francisco, O. / Harder-Viddal, C. / Roshko, R. / Heide, F. / Sidhu, S. / Khajehpour, M. / Leslie, J. / Palace, V. / Tomy, G.T. / Stetefeld, J.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Tetrabrachion
B: Tetrabrachion
C: Tetrabrachion
D: Tetrabrachion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4669
Polymers23,5954
Non-polymers8715
Water1,964109
1
A: Tetrabrachion
B: Tetrabrachion
hetero molecules

A: Tetrabrachion
B: Tetrabrachion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,52810
Polymers23,5954
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
2
C: Tetrabrachion
D: Tetrabrachion
hetero molecules

C: Tetrabrachion
D: Tetrabrachion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4048
Polymers23,5954
Non-polymers8094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Unit cell
Length a, b, c (Å)35.023, 76.995, 35.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11C-227-

HOH

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Components

#1: Protein
Tetrabrachion


Mass: 5898.720 Da / Num. of mol.: 4 / Fragment: UNP residues 1238-1287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylothermus marinus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q54436
#2: Chemical
ChemComp-8P0 / pyrene


Mass: 202.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H10
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350,0.1M Bis-Tris pH 5.5, 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.055→19.25 Å / Num. obs: 11575 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.096 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FE6

1fe6


Resolution: 2.055→17.831 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 580 5.03 %Random Selection
Rwork0.2125 ---
obs0.2147 11521 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.055→17.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 68 109 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041594
X-RAY DIFFRACTIONf_angle_d0.4082175
X-RAY DIFFRACTIONf_dihedral_angle_d22.278947
X-RAY DIFFRACTIONf_chiral_restr0.034270
X-RAY DIFFRACTIONf_plane_restr0.002267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.055-2.26140.29151440.23882662X-RAY DIFFRACTION98
2.2614-2.58780.24121620.21632733X-RAY DIFFRACTION100
2.5878-3.25710.28681420.22562775X-RAY DIFFRACTION99
3.2571-17.83180.23831320.19482771X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96690.0035-0.18237.3249-0.30822.0990.0790.0967-0.0796-0.8087-0.1299-0.04270.02380.0722-0.00360.12550.00090.00550.1843-0.00450.069737.365237.3531-6.9964
21.7554-0.07730.12116.7754-0.44362.08350.0496-0.0248-0.06550.1556-0.1503-0.76960.08970.1120.07360.0906-0.0027-0.00830.20740.00020.109642.048236.62412.4389
31.99720.09290.1887.08230.30331.97680.1910.08120.4322-0.5074-0.32670.3587-0.3946-0.16330.02660.14320.0257-0.01040.22910.02060.245.539748.73815.2636
41.9248-0.0411-0.18237.6607-0.41822.10170.0877-0.13650.38610.571-0.24490.2493-0.45350.00420.13590.20940.00070.01040.2347-0.02950.146550.190148.902624.5621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 52 )
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 52 )
3X-RAY DIFFRACTION3chain 'C' and (resid 4 through 51 )
4X-RAY DIFFRACTION4chain 'D' and (resid 4 through 52 )

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