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- PDB-6egm: Crystal Structure of a de novo Three-stranded Coiled Coil Peptide... -

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Basic information

Entry
Database: PDB / ID: 6egm
TitleCrystal Structure of a de novo Three-stranded Coiled Coil Peptide Containing D-Leu in a d-site Position of a Tris-thiolate Binding Site
ComponentsApo-(GRAND CoilSerL16CL19(DLE))3
KeywordsDE NOVO PROTEIN / Three-stranded Coiled Coil Peptide / D-Leu / Metalloprotein / Engineered Protein / D-amino acids
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

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Assembly

Deposited unit
A: Apo-(GRAND CoilSerL16CL19(DLE))3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1802
Polymers4,1151
Non-polymers651
Water79344
1
A: Apo-(GRAND CoilSerL16CL19(DLE))3
hetero molecules

A: Apo-(GRAND CoilSerL16CL19(DLE))3
hetero molecules

A: Apo-(GRAND CoilSerL16CL19(DLE))3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5416
Polymers12,3443
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4390 Å2
ΔGint-113 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.898, 37.898, 140.667
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-222-

HOH

21A-241-

HOH

31A-243-

HOH

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Components

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


Mass: 4114.800 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, lithium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 3615 / % possible obs: 99.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Χ2: 1.054 / Net I/σ(I): 19.6 / Num. measured all: 49750
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.8680.1243170.990.0490.1341.169100
1.86-1.980.1153310.9930.0440.1231.2100
1.9-1.9380.1053090.9960.0410.1131.177100
1.93-1.9780.0953480.9940.0360.1021.14100
1.97-2.017.90.0893280.9950.0350.0961.13100
2.01-2.067.70.0873360.9950.0340.0941.204100
2.06-2.117.90.0793330.9960.0310.0851.146100
2.11-2.177.60.0783190.9960.0310.0841.133100
2.17-2.237.40.0683440.9960.0280.0741.134100
2.23-2.317.50.073220.9960.0280.0751.139100
2.31-2.397.30.0633440.9970.0250.0681.009100
2.39-2.487.10.0633270.9970.0260.0681.057100
2.48-2.67.20.0653240.9960.0270.0711.078100
2.6-2.737.30.0643300.9970.0250.0691.047100
2.73-2.97.40.0623500.9970.0250.0671.031100
2.9-3.137.60.0563250.9970.0220.060.879100
3.13-3.447.10.0593360.9970.0250.0640.89299.4
3.44-3.947.30.0543240.9980.0210.0580.822100
3.94-4.977.60.0523280.9980.020.0560.80899.4
4.97-507.40.0543080.9960.0210.0580.79991.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 1.84→23.44 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9285 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.206 190 5.26 %RANDOM
Rwork0.2006 ---
obs0.201 3615 99.45 %-
Displacement parametersBiso max: 100.53 Å2 / Biso mean: 30.51 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.5579 Å20 Å20 Å2
2---1.5579 Å20 Å2
3---3.1158 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: final / Resolution: 1.84→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms282 0 1 44 327
Biso mean--17.78 31.94 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes10HARMONIC2
X-RAY DIFFRACTIONt_gen_planes37HARMONIC5
X-RAY DIFFRACTIONt_it284HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion35SEMIHARMONIC5
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_contact388SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d284HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg378HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion2.97
LS refinement shellResolution: 1.84→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.1981 45 4.5 %
Rwork0.1527 956 -
all0.1549 1001 -
obs--99.45 %
Refinement TLS params.Method: refined / Origin x: 5.019 Å / Origin y: 1.352 Å / Origin z: 26.9277 Å
111213212223313233
T0.0153 Å2-0.0142 Å20.0131 Å2-0.0047 Å20.0042 Å2---0.0234 Å2
L-0.2007 °20.0382 °20.0349 °2-0.47 °2-3.2335 °2--13.1295 °2
S-0.0716 Å °0.0513 Å °-0.0185 Å °-0.0604 Å °0.1062 Å °-0.0413 Å °-0.0139 Å °-0.2012 Å °-0.0347 Å °
Refinement TLS groupSelection details: {A|1 - 36}

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