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- PDB-6b87: Crystal structure of transmembrane protein TMHC2_E -

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Basic information

Entry
Database: PDB / ID: 6b87
TitleCrystal structure of transmembrane protein TMHC2_E
ComponentsTMHC2_E
KeywordsMEMBRANE PROTEIN / De novo design / transmembrane protein / helical bundle / dimer
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.947 Å
AuthorsLu, P. / DiMaio, F. / Min, D. / Wei, K.Y. / Bowie, J. / Baker, D.
CitationJournal: Science / Year: 2018
Title: Accurate computational design of multipass transmembrane proteins.
Authors: Lu, P. / Min, D. / DiMaio, F. / Wei, K.Y. / Vahey, M.D. / Boyken, S.E. / Chen, Z. / Fallas, J.A. / Ueda, G. / Sheffler, W. / Mulligan, V.K. / Xu, W. / Bowie, J.U. / Baker, D.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TMHC2_E
B: TMHC2_E
C: TMHC2_E
D: TMHC2_E


Theoretical massNumber of molelcules
Total (without water)53,1764
Polymers53,1764
Non-polymers00
Water00
1
A: TMHC2_E

A: TMHC2_E


Theoretical massNumber of molelcules
Total (without water)26,5882
Polymers26,5882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Buried area3970 Å2
ΔGint-42 kcal/mol
Surface area11470 Å2
MethodPISA
2
B: TMHC2_E

B: TMHC2_E


Theoretical massNumber of molelcules
Total (without water)26,5882
Polymers26,5882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area3630 Å2
ΔGint-42 kcal/mol
Surface area10040 Å2
MethodPISA
3
C: TMHC2_E
D: TMHC2_E


Theoretical massNumber of molelcules
Total (without water)26,5882
Polymers26,5882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-48 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.485, 121.602, 51.952
Angle α, β, γ (deg.)90.00, 119.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TMHC2_E


Mass: 13293.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05 M magnesium acetate tetrahydrate, 0.05 M sodium acetate, pH 5.4, 30% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 10899 / % possible obs: 92.5 % / Redundancy: 3.5 % / Net I/σ(I): 9.6
Reflection shellHighest resolution: 2.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.947→36.942 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 1106 10.17 %
Rwork0.2576 --
obs0.2595 10872 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.947→36.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 0 0 3068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113079
X-RAY DIFFRACTIONf_angle_d1.2574191
X-RAY DIFFRACTIONf_dihedral_angle_d10.6431119
X-RAY DIFFRACTIONf_chiral_restr0.069593
X-RAY DIFFRACTIONf_plane_restr0.007494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9466-3.08060.32591000.2932856X-RAY DIFFRACTION64
3.0806-3.24290.326970.28571053X-RAY DIFFRACTION80
3.2429-3.4460.33211580.2871248X-RAY DIFFRACTION94
3.446-3.71180.36861430.25851318X-RAY DIFFRACTION99
3.7118-4.08490.27771440.25421313X-RAY DIFFRACTION100
4.0849-4.6750.23041610.21461326X-RAY DIFFRACTION100
4.675-5.88610.3181530.281306X-RAY DIFFRACTION100
5.8861-36.94440.23811500.25971346X-RAY DIFFRACTION98

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