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- PDB-4p6l: Crystal Structure of the Computationally Designed Transmembrane M... -

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Entry
Database: PDB / ID: 4p6l
TitleCrystal Structure of the Computationally Designed Transmembrane Metallotransporter in Octyl Glucoside
ComponentsComputationally Designed Transporter of Zn(II) and proton
KeywordsDE NOVO PROTEIN / transmembrane / transporter / de-novo designed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsJoh, N.H. / Acharya, R. / DeGrado, W.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)7U01AI074571 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3F32GM096727 United States
CitationJournal: Science / Year: 2014
Title: De novo design of a transmembrane Zn2+-transporting four-helix bundle.
Authors: Joh, N.H. / Wang, T. / Bhate, M.P. / Acharya, R. / Wu, Y. / Grabe, M. / Hong, M. / Grigoryan, G. / DeGrado, W.F.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: 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:
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Assembly

Deposited unit
A: Computationally Designed Transporter of Zn(II) and proton
B: Computationally Designed Transporter of Zn(II) and proton


Theoretical massNumber of molelcules
Total (without water)5,9072
Polymers5,9072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.120, 87.120, 87.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
DetailsTHE BIOLOGICAL UNIT WAS DETERMINED BY COMBINED APPROACH OF COMPUTATIONAL DESIGN, ANALYTICAL ULTRACENTRIFUGATION AND 19F-CODEX VIA SOLID-STATE NMR. AS PER THE AUTHORS THIS TETRAMERIC ASSEMBLY IS REPORTED IN THE SEPARATE ENTRY (PDB ID: 2MUZ) FOR THE SOLID-STATE NMR MODEL ACCOMPANIED BY THE PAPER THAT CITES THIS PDB

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Components

#1: Protein/peptide Computationally Designed Transporter of Zn(II) and proton


Mass: 2953.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.66 Å3/Da / Density % sol: 73.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1:1 (vol.) mixture of OG-bound Rocker (1 mM peptide, 1 mM CoSO4, 50 mM OG) and the well solution (360 mM LiCl, 100 mM sodium citrate (pH 5.6), 28 % (w/v) PEG 400, 1.56M 1,2-hexanedediol) ...Details: 1:1 (vol.) mixture of OG-bound Rocker (1 mM peptide, 1 mM CoSO4, 50 mM OG) and the well solution (360 mM LiCl, 100 mM sodium citrate (pH 5.6), 28 % (w/v) PEG 400, 1.56M 1,2-hexanedediol) inverted above the well solution and incubated at room temperature over 2.5 weeks

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.8→61.6 Å / Num. obs: 2699 / % possible obs: 95.5 % / Redundancy: 6.3 % / Net I/σ(I): 13.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.803→43.56 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 41.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3032 261 10.05 %
Rwork0.2924 --
obs0.2942 2598 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms422 0 0 0 422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002434
X-RAY DIFFRACTIONf_angle_d0.399588
X-RAY DIFFRACTIONf_dihedral_angle_d10.225144
X-RAY DIFFRACTIONf_chiral_restr0.01764
X-RAY DIFFRACTIONf_plane_restr0.00170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-3.53130.40691230.36221131X-RAY DIFFRACTION90
3.5313-43.56520.28261380.27811206X-RAY DIFFRACTION94

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