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- PDB-6egn: Crystal Structure of a Three-stranded Coiled Coil Peptide Contain... -

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Basic information

Entry
Database: PDB / ID: 6egn
TitleCrystal Structure of a Three-stranded Coiled Coil Peptide Containing a Trigonal Planar Hg(II)S3 Site Modified by D-Leu in the Second Coordination Sphere
ComponentsHg(II)(GRAND CoilSerL16CL19(DLE))3-
KeywordsDE NOVO PROTEIN / De Novo Three-stranded Helical Coiled Coil Peptide / Hg(II)S3 complex / D-amino acids / D-Leu / Trigonal Planar Hg(II) Structure
Function / homology: / PROLINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hg(II)(GRAND CoilSerL16CL19(DLE))3-
B: Hg(II)(GRAND CoilSerL16CL19(DLE))3-
C: Hg(II)(GRAND CoilSerL16CL19(DLE))3-
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,13912
Polymers12,4173
Non-polymers3,7229
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-144 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.636, 80.508, 88.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 3 molecules ABC

#1: Protein/peptide Hg(II)(GRAND CoilSerL16CL19(DLE))3-


Mass: 4138.846 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 174 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


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


Mass: 18.015 Da / Num. of mol.: 165 / 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: 4.69 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M L-Proline, 0.1 M HEPES, pH 7.5, 10% w/v PEG3350
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 20279 / % possible obs: 97 % / Redundancy: 8.8 % / Biso Wilson estimate: 36.53 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / Χ2: 0.96 / Net I/σ(I): 6.7 / Num. measured all: 178615
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.878.20.46810110.9050.1740.5010.63799.4
1.87-1.9190.42310350.9270.1520.4510.69699.6
1.91-1.949.30.379910.9340.1320.3940.74199.5
1.94-1.989.50.32910090.9640.1160.350.72299.4
1.98-2.039.50.28910650.9550.1010.3070.78199.4
2.03-2.079.20.2499950.9680.0890.2650.84199.1
2.07-2.129.40.21510070.9620.0770.2290.89199.2
2.12-2.189.30.19410330.9780.070.2070.91898.8
2.18-2.259.20.1710030.9750.0620.1820.94898.6
2.25-2.329.20.15510230.9770.0580.1660.9698.1
2.32-2.48.90.1469930.9790.0550.1571.05197.7
2.4-2.590.13910390.9860.0520.1491.06698.1
2.5-2.618.80.1299880.9840.0490.1381.10197
2.61-2.758.90.12210190.9890.0460.1311.13897
2.75-2.928.90.1169990.9830.0450.1251.13896.1
2.92-3.158.60.10810130.9850.0410.1171.18195.7
3.15-3.468.50.09510060.9890.0360.1021.14395.1
3.46-3.9680.08910150.9920.0340.0961.14395
3.96-4.997.80.08610210.990.0340.0931.09893.4
4.99-507.10.08710140.9870.0370.0951.14986.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
HKL-2000data collection
RefinementResolution: 1.84→19.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.949 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.209 980 4.85 %RANDOM
Rwork0.197 ---
obs0.198 20219 96.2 %-
Displacement parametersBiso max: 147.85 Å2 / Biso mean: 46.02 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1--7.19 Å20 Å20 Å2
2---1.391 Å20 Å2
3---8.5809 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.84→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 38 165 1065
Biso mean--95.83 54.75 -
Num. residues----114
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d388SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes131HARMONIC5
X-RAY DIFFRACTIONt_it955HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1184SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d967HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1291HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion18.52
LS refinement shellResolution: 1.84→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.274 127 4.52 %
Rwork0.227 2682 -
all0.229 2809 -
obs--93.29 %
Refinement TLS params.

L11: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0074-1.4675.1197-4.79364.2396-0.0044-0.2824-0.14540.2124-0.5755-0.6338-0.07280.50350.5798-0.0708-0.0621-0.0630.04710.12550.03152.50265.292417.9375
20.1323-0.56552.8621-3.84534.5143-0.02450.0176-0.08760.15740.0476-0.0275-0.0799-0.1445-0.023-0.0003-0.0238-0.0281-0.0050.0476-0.0074-6.89845.240215.1706
31.2519-1.27041.0749-2.13543.4425-0.1215-0.0293-0.1765-0.3627-0.103-0.22950.6890.08650.2245-0.01950.03760.0557-0.00950.05290.0502-1.35630.015210.7418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|*}A0 - 37
2X-RAY DIFFRACTION2{B|*}B0 - 37
3X-RAY DIFFRACTION3{C|*}C0 - 37

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