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- PDB-6ego: Crystal Structure of a de Novo Three-stranded Coiled Coil Peptide... -

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Basic information

Entry
Database: PDB / ID: 6ego
TitleCrystal Structure of a de Novo Three-stranded Coiled Coil Peptide Containing an Ala Residue in the Second Coordination Sphere of the Hg(II)S3 Binding Site
ComponentsHg(II)(GRAND CoilSerL12AL16C)3-
KeywordsDE NOVO PROTEIN / De Novo Three-stranded Helical Coiled Coil Peptide / Tris-thiolate Hg(II) Complex / Trigonal Planar Hg(II)S3
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsRuckthong, L. / Stuckey, J.A. / Pecoraro, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01ES012236 United States
CitationJournal: Chemistry / Year: 2019
Title: How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation.
Authors: Ruckthong, L. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.title ..._citation.journal_id_ISSN / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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

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Assembly

Deposited unit
A: Hg(II)(GRAND CoilSerL12AL16C)3-
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3393
Polymers4,0731
Non-polymers2662
Water27015
1
A: Hg(II)(GRAND CoilSerL12AL16C)3-
hetero molecules

A: Hg(II)(GRAND CoilSerL12AL16C)3-
hetero molecules

A: Hg(II)(GRAND CoilSerL12AL16C)3-
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0169
Polymers12,2183
Non-polymers7986
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 area4390 Å2
ΔGint-114 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.186, 38.186, 142.345
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-102-

HG

21A-213-

HOH

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Components

#1: Protein/peptide Hg(II)(GRAND CoilSerL12AL16C)3-


Mass: 4072.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.5, 25% PEG1000 / PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 3271 / % possible obs: 99.4 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Χ2: 1.027 / Net I/σ(I): 8.9 / Num. measured all: 47352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9612.70.5571470.9490.150.5780.49496.7
1.96-216.10.4861630.9730.1210.5010.515100
2-2.0415.90.3911670.9730.0990.4040.569100
2.04-2.0815.70.3421530.9840.0870.3530.584100
2.08-2.1215.90.281560.9860.0720.2890.683100
2.12-2.1716.30.2191580.9920.0550.2260.71100
2.17-2.2315.30.191660.9930.0490.1960.8100
2.23-2.2915.90.1621640.9950.0420.1680.866100
2.29-2.3615.50.1581580.9950.0410.1630.957100
2.36-2.4315.60.1291630.9950.0340.1340.995100
2.43-2.5215.40.1191640.9960.0310.1231.072100
2.52-2.6215.50.1191570.9970.0310.1231.195100
2.62-2.7415.10.111680.9980.0290.1141.267100
2.74-2.8814.80.1051650.9970.0280.1091.368100
2.88-3.0614.20.0931600.9980.0260.0961.41100
3.06-3.3140.0821670.9980.0230.0851.557100
3.3-3.63130.0771630.9950.0240.0811.458100
3.63-4.1612.20.0751760.9980.0220.0781.493100
4.16-5.24120.0731720.9980.0220.0761.38499.4
5.24-509.30.0781840.9960.0270.0831.55992.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KB2

5kb2


Resolution: 1.93→24.225 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.2524 185 5.66 %
Rwork0.2201 --
obs0.2223 3266 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 47.3637 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 1.93→24.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms284 0 2 15 301
Biso mean--41.1 48.72 -
Num. residues----36

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