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- PDB-6naf: De novo designed homo-trimeric amantadine-binding protein -

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Basic information

Entry
Database: PDB / ID: 6naf
TitleDe novo designed homo-trimeric amantadine-binding protein
Componentsamantadine-binding protein
KeywordsDE NOVO PROTEIN / helical bundle / trimer / amantadine-binding protein
Function / homology(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / DEUTERATED WATER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.923 Å
AuthorsSelvaraj, B. / Park, J. / Cuneo, M.J. / Myles, D.A.A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Elife / Year: 2019
Title: De novo design of a homo-trimeric amantadine-binding protein.
Authors: Park, J. / Selvaraj, B. / McShan, A.C. / Boyken, S.E. / Wei, K.Y. / Oberdorfer, G. / DeGrado, W. / Sgourakis, N.G. / Cuneo, M.J. / Myles, D.A. / Baker, D.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: amantadine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3143
Polymers9,1401
Non-polymers1742
Water73941
1
A: amantadine-binding protein
hetero molecules

A: amantadine-binding protein
hetero molecules

A: amantadine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9419
Polymers27,4193
Non-polymers5236
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area18420 Å2
ΔGint-50 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 50.610, 68.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-101-

308

21A-101-

308

31A-102-

NA

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Components

#1: Protein amantadine-binding protein


Mass: 9139.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pPpARG4
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#2: Chemical ChemComp-308 / (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Amantadine


Mass: 151.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antagonist*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: D2O / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 9% PEG6000, 0.1 M citric acid, pH 4.0 / PH range: 4-5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981N
22981N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5417
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D22.8-4.5
Detector
TypeIDDetectorDate
RIGAKU1IMAGE PLATEDec 9, 2017
MAATEL IMAGINE2IMAGE PLATEJun 12, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54171
22.81
34.51
Reflection

Entry-ID: 6NAF

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.92-68.82765510017.80.09123.2
2.3-36.72263973.540.14328.7
Reflection shell
Resolution (Å)Num. unique obsDiffraction-ID% possible all
1.92-9.0276861100
2.5-7.2730912

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
LAUEGENdata reduction
LSCALEdata scaling
PHASERphasing
Refinement

SU ML: 0.16 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.84 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: PDB entry 6N9H

6n9h

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.923-36.969X-RAY DIFFRACTION0.20390.17480.1777770765510.0699.871.38
2.5-27.065NEUTRON DIFFRACTION0.31790.27710.280126126399.8975.3423.7
Refinement stepCycle: LAST / Resolution: 1.923→36.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 0 12 41 649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131390
X-RAY DIFFRACTIONf_angle_d2.0012433
X-RAY DIFFRACTIONf_dihedral_angle_d14.512566
X-RAY DIFFRACTIONf_chiral_restr0.073102
X-RAY DIFFRACTIONf_plane_restr0.01214
NEUTRON DIFFRACTIONf_bond_d0.0131390
NEUTRON DIFFRACTIONf_angle_d2.0012433
NEUTRON DIFFRACTIONf_dihedral_angle_d14.512566
NEUTRON DIFFRACTIONf_chiral_restr0.073102
NEUTRON DIFFRACTIONf_plane_restr0.01214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9231-2.07160.21391470.19091368X-RAY DIFFRACTION100
2.0716-2.28010.18341560.18241377X-RAY DIFFRACTION100
2.2801-2.60990.20961580.1741362X-RAY DIFFRACTION100
2.6099-3.28790.21421470.19071389X-RAY DIFFRACTION100
3.2879-36.97560.20011620.15981389X-RAY DIFFRACTION99
2.5002-3.14920.33891030.3266986NEUTRON DIFFRACTION63
3.1492-27.0670.3091580.25181392NEUTRON DIFFRACTION88

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