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- PDB-7r6h: RHCC in complex with o-carborane -

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Basic information

Entry
Database: PDB / ID: 7r6h
TitleRHCC in complex with o-carborane
ComponentsTetrabrachion
KeywordsTRANSPORT PROTEIN / Right-handed coiled coil / Carborane / Nanotube
Function / homologyTetrabrachion / Tetrabrachion, parallel right-handed coiled coil domain / Tetrabrachion / membrane / ortho-carborane / Tetrabrachion
Function and homology information
Biological speciesStaphylothermus marinus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHeide, F. / McDougall, M. / Stetefeld, J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)201610PJT-152935 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-004954-2017 Canada
CitationJournal: Sci Rep / Year: 2021
Title: Boron rich nanotube drug carrier system is suited for boron neutron capture therapy.
Authors: Heide, F. / McDougall, M. / Harder-Viddal, C. / Roshko, R. / Davidson, D. / Wu, J. / Aprosoff, C. / Moya-Torres, A. / Lin, F. / Stetefeld, J.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrabrachion
B: Tetrabrachion
C: Tetrabrachion
D: Tetrabrachion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9917
Polymers23,5954
Non-polymers3963
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-85 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.450, 55.920, 110.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 BL21 (bacteria) / References: UniProt: Q54436
#2: Chemical ChemComp-1KW / ortho-carborane


Mass: 132.131 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2B10 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.8 % / Description: Rod-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M ammonium acetate, 0.05 M sodium cacodylate trihydrate, 10% v/v 2-propanol, 0.015 M magnesium acetate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 28, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→18.69 Å / Num. obs: 22224 / % possible obs: 98.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 21.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.084 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 8 / Num. unique obs: 5798 / CC1/2: 0.991 / Rrim(I) all: 0.208 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YBK

1ybk


Resolution: 2.2→18.69 Å / SU ML: 0.179 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0921
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 1502 7.3 %
Rwork0.2223 19076 -
obs0.2253 20578 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 36 59 1712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271720
X-RAY DIFFRACTIONf_angle_d0.38852577
X-RAY DIFFRACTIONf_chiral_restr0.0344293
X-RAY DIFFRACTIONf_plane_restr0.005281
X-RAY DIFFRACTIONf_dihedral_angle_d5.2005249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.26591370.24981770X-RAY DIFFRACTION99.01
2.27-2.350.36011340.25091744X-RAY DIFFRACTION99.1
2.35-2.450.28621470.23941748X-RAY DIFFRACTION99.16
2.45-2.560.28671380.22311737X-RAY DIFFRACTION99.42
2.56-2.690.23571480.21921714X-RAY DIFFRACTION99.1
2.69-2.860.30851440.24221765X-RAY DIFFRACTION98.71
2.86-3.080.27961410.22831694X-RAY DIFFRACTION97.66
3.08-3.390.26721280.24231703X-RAY DIFFRACTION97.71
3.39-3.870.23491120.20721758X-RAY DIFFRACTION97.91
3.87-4.870.21481230.17791737X-RAY DIFFRACTION98.05
4.87-18.690.28031500.24111706X-RAY DIFFRACTION98.1
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)
12.18681450904-0.879033569331-2.507627352110.5080490248211.134853003612.96740450348-0.105372256048-0.234242742277-0.03254728955670.1737361906380.123852815794-0.03470270732340.330640367730.03471673252880.03408060186850.1783407549320.0002080663825650.003026295867090.73426429425-0.004853098075160.1163634907215.5277001915-5.7248792568716.1016846303
21.007747893130.16499871848-0.1135479291590.371157426425-0.02146585566930.9738640117260.0404778588874-0.142598420086-0.08274904664630.0979670507859-0.0066173346404-0.0227646122990.129791399795-0.171155538651-0.1101214630630.152829285587-0.0469674498488-0.05462611571410.733626341472-0.07026668917310.123353248249.34087744202-3.063497778967.87712543538
36.32564057393-0.796718451733-4.60505496541.006487401350.5265786960973.929177367050.2917036816790.2616762511540.702569423252-0.05960540732690.03074457892980.0487157406693-0.497780766085-0.348271394658-0.315517104360.1700843552530.06340594429340.0239289525360.548972413155-0.03144840122320.20193357790313.4632636066.659223376997.96581260091
43.96260431454-0.753295684512-3.006786999931.122887380110.4769292263523.303274593910.230672826281-0.1013588783160.2764963774450.135434125052-0.0326912547596-0.0533465537357-0.345995548349-0.00471129568727-0.1302622232950.198305834955-0.02690247186220.00178957463240.613624344422-0.08654368608670.11437181023219.1888208214.0086357157616.264184686
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 52 )AA1 - 521 - 52
22chain 'B' and (resid 2 through 52 )BB2 - 521 - 51
33chain 'C' and (resid 3 through 52 )CC3 - 521 - 50
44chain 'D' and (resid 1 through 52 )DD1 - 521 - 52

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