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- PDB-2jgo: Structure of the arsenated de novo designed peptide Coil Ser L9C -

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Basic information

Entry
Database: PDB / ID: 2jgo
TitleStructure of the arsenated de novo designed peptide Coil Ser L9C
ComponentsCOIL SER L9C
KeywordsDE NOVO PROTEIN / DE NOVO DESIGN / THREE-STRANDED COILED COIL / ARSENIC(III) BINDING PROTEIN
Function / homologyARSENIC
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsTouw, D.S. / Nordman, C.E. / Stuckey, J.A. / Pecoraro, V.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Identifying Important Structural Characteristics of Arsenic Resistance Proteins by Using Designed Three-Stranded Coiled Coils.
Authors: Touw, D.S. / Nordman, C.E. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionFeb 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 21, 2016Group: Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COIL SER L9C
B: COIL SER L9C
C: COIL SER L9C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3148
Polymers9,9783
Non-polymers3375
Water95553
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-21.8 kcal/mol
Surface area7060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.284, 29.416, 44.197
Angle α, β, γ (deg.)90.00, 119.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

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Components

#1: Protein/peptide COIL SER L9C


Mass: 3325.850 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 43.9 % / Description: NONE
Crystal growpH: 8
Details: 100 MM IMIDAZOLE PH 8.0 200 MM ZINC ACETATE 30% V/V PEG-400

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→13.7 Å / Num. obs: 8137 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC6refinement
HKL-2000data reduction
SCALEPACKdata scaling
GENPATphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COI

1coi


Resolution: 1.81→13.74 Å / SU B: 2.778 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25665 373 4.6 %RANDOM
Rwork0.19843 ---
obs0.20114 7686 99.15 %-
Displacement parametersBiso mean: 18.066 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.81→13.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 5 53 760

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