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- PDB-6b85: Crystal structure of transmembrane protein TMHC4_R -

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Basic information

Entry
Database: PDB / ID: 6b85
TitleCrystal structure of transmembrane protein TMHC4_R
ComponentsTMHC4_R
KeywordsMEMBRANE PROTEIN / De novo design / multipass transmembrane protein / helical bundle / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.889 Å
AuthorsLu, P. / DiMaio, F. / Min, D. / Bowie, J. / Wei, K.Y. / 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 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Mar 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
J: TMHC4_R
A: TMHC4_R
B: TMHC4_R
C: TMHC4_R


Theoretical massNumber of molelcules
Total (without water)100,4894
Polymers100,4894
Non-polymers00
Water00
1
J: TMHC4_R

J: TMHC4_R

J: TMHC4_R

J: TMHC4_R


Theoretical massNumber of molelcules
Total (without water)100,4894
Polymers100,4894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area14280 Å2
ΔGint-143 kcal/mol
Surface area41230 Å2
MethodPISA
2
A: TMHC4_R

A: TMHC4_R

A: TMHC4_R

A: TMHC4_R


Theoretical massNumber of molelcules
Total (without water)100,4894
Polymers100,4894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area13380 Å2
ΔGint-161 kcal/mol
Surface area42140 Å2
MethodPISA
3
B: TMHC4_R

B: TMHC4_R

B: TMHC4_R

B: TMHC4_R


Theoretical massNumber of molelcules
Total (without water)100,4894
Polymers100,4894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area14370 Å2
ΔGint-145 kcal/mol
Surface area41330 Å2
MethodPISA
4
C: TMHC4_R

C: TMHC4_R

C: TMHC4_R

C: TMHC4_R


Theoretical massNumber of molelcules
Total (without water)100,4894
Polymers100,4894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area13370 Å2
ΔGint-159 kcal/mol
Surface area42440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.240, 80.240, 251.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
TMHC4_R


Mass: 25122.281 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: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30% v/v PEG400, 100 mM MOPS, pH 7.0, 100 mM sodium chloride, 10 mM DDAO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 14545 / % possible obs: 99.6 % / Redundancy: 12 % / Net I/σ(I): 18.2
Reflection shellHighest resolution: 3.9 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.889→46.992 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3224 1448 10.05 %
Rwork0.2913 --
obs0.294 14406 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.889→46.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 0 0 6764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0216848
X-RAY DIFFRACTIONf_angle_d1.5589268
X-RAY DIFFRACTIONf_dihedral_angle_d9.3632604
X-RAY DIFFRACTIONf_chiral_restr0.1161128
X-RAY DIFFRACTIONf_plane_restr0.0091144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8893-4.02830.37021450.33581265X-RAY DIFFRACTION96
4.0283-4.18950.34221430.30831302X-RAY DIFFRACTION99
4.1895-4.380.36041460.32741296X-RAY DIFFRACTION100
4.38-4.61070.34571420.30711305X-RAY DIFFRACTION100
4.6107-4.89930.33131480.30491300X-RAY DIFFRACTION99
4.8993-5.27710.40821430.34251291X-RAY DIFFRACTION99
5.2771-5.80730.37681500.3421283X-RAY DIFFRACTION98
5.8073-6.64570.32931460.29971326X-RAY DIFFRACTION100
6.6457-8.36510.27261390.26951310X-RAY DIFFRACTION100
8.3651-46.99580.29781460.26571280X-RAY DIFFRACTION95

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