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- PDB-4p6k: Crystal Structure of the Computationally Designed Transmembrane M... -

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Entry
Database: PDB / ID: 4p6k
TitleCrystal Structure of the Computationally Designed Transmembrane Metallotransporter with 4-bromophenylalanine in Lipidic Cubic Phase
ComponentsComputationally Designed Transporter of Zn(II) and Proton
KeywordsDE NOVO PROTEIN / transmembrane / transporter / lipidic cubic phase / de-novo designed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 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)7U01AI074571-05 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,0161
Polymers3,0161
Non-polymers00
Water0
1
A: Computationally Designed Transporter of Zn(II) and Proton

A: Computationally Designed Transporter of Zn(II) and Proton


Theoretical massNumber of molelcules
Total (without water)6,0332
Polymers6,0332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.870, 46.870, 60.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
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: 3016.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Compound detailsBR HAS ZERO OCCUPANCY IN 4BF. THE AUTHORS COLLECTED DATA FROM THE SINGLE CRYSTAL USING THE ...BR HAS ZERO OCCUPANCY IN 4BF. THE AUTHORS COLLECTED DATA FROM THE SINGLE CRYSTAL USING THE SYNCHROTRON BEAM TUNED AT THE BROMINE EDGE. BROMINE IS VERY LABILE UNDER RADIATION AND READILY DEGRADES UPON REPEATED DATA COLLECTION. THE LAST DATASET IS COLLECTED BY USING INCREASED EXPOSURE TO ATTAIN DIFFRACTIONS AT THE HIGH-RESOLUTION SPACE. THIS RESULTS IN OCCUPANCY OF 0 FOR THE MENTIONED BROMINE. THIS STUDY HAS BEEN CONFIRMED BY MASS SPEC

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase
Details: 100 nl boluses containing monoolein-bound Rocker Br-Phe2 (4 mM peptide, 60% (vol) monoolein, 6 mM ZnSO4) immersed in 1 ?l of precipitation buffer (0.05 M Li2SO4, 0.1 M tricine (pH 7.4), 7 % ...Details: 100 nl boluses containing monoolein-bound Rocker Br-Phe2 (4 mM peptide, 60% (vol) monoolein, 6 mM ZnSO4) immersed in 1 ?l of precipitation buffer (0.05 M Li2SO4, 0.1 M tricine (pH 7.4), 7 % (w/v) PEG 3000) incubated in 0.1-mm-deep wells at room temperature over a month

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 1601 / % possible obs: 89.4 % / Redundancy: 10.8 % / Net I/σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 25-residue-long idealized helix

Resolution: 2.704→37.076 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3045 161 10.06 %
Rwork0.2947 --
obs0.296 1601 89.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.704→37.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms211 0 0 0 211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003217
X-RAY DIFFRACTIONf_angle_d0.386294
X-RAY DIFFRACTIONf_dihedral_angle_d11.07371
X-RAY DIFFRACTIONf_chiral_restr0.02132
X-RAY DIFFRACTIONf_plane_restr0.00135

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