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- PDB-7n2y: Crystal Structure of a de Novo Three-stranded Coiled Coil Peptide... -

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Basic information

Entry
Database: PDB / ID: 7n2y
TitleCrystal Structure of a de Novo Three-stranded Coiled Coil Peptide Containing a dual Tris-thiolate Binding Site for Heavy Metal Complexes
ComponentsApo-(GRAND CoilSerL16CL23C)3
KeywordsBIOSYNTHETIC PROTEIN / Three-straded coiled coil 3SCC Tris-thiolate sites de novo peptide Heavy metal binding
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsRuckthong, L. / Stuckey, J.A. / Pecoraro, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141086 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead.
Authors: Pinter, T.B.J. / Ruckthong, L. / Stuckey, J.A. / Deb, A. / Penner-Hahn, J.E. / Pecoraro, V.L.
History
DepositionMay 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apo-(GRAND CoilSerL16CL23C)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1702
Polymers4,1051
Non-polymers651
Water43224
1
A: Apo-(GRAND CoilSerL16CL23C)3
hetero molecules

A: Apo-(GRAND CoilSerL16CL23C)3
hetero molecules

A: Apo-(GRAND CoilSerL16CL23C)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5116
Polymers12,3143
Non-polymers1963
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 area4250 Å2
ΔGint-118 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.328, 38.328, 141.824
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-209-

HOH

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Components

#1: Protein/peptide Apo-(GRAND CoilSerL16CL23C)3


Mass: 4104.785 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 and 25% (w/v) PEG-1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.08→20 Å / Num. obs: 2603 / % possible obs: 99.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 47.19 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Χ2: 1.056 / Net I/σ(I): 8.8 / Num. measured all: 38222
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.1215.40.7131130.9460.1810.7360.73100
2.12-2.1515.30.5241350.9760.1340.5410.761100
2.15-2.215.50.4491190.9810.1140.4640.795100
2.2-2.2415.60.3661290.980.0930.3770.816100
2.24-2.2915.70.2731280.9920.0690.2820.884100
2.29-2.3415.70.2741240.9910.0690.2830.844100
2.34-2.415.50.2411370.9930.0620.2490.903100
2.4-2.4715.90.2141190.9930.0540.2211100
2.47-2.5415.70.1791260.9930.0460.1851.044100
2.54-2.6215.20.1741300.9970.0450.1791.016100
2.62-2.7115.30.1491280.9970.0380.1541.126100
2.71-2.8215.10.1341280.9960.0350.1381.135100
2.82-2.9514.60.1211320.9960.0330.1261.358100
2.95-3.114.40.1061270.9980.0290.111.298100
3.1-3.313.80.0881320.9990.0250.0921.356100
3.3-3.5513.80.0781330.9970.0220.0821.367100
3.55-3.9113.90.0721310.9970.020.0751.225100
3.91-4.4713.30.0661370.9990.0180.0691.124100
4.47-5.6113.10.06613910.0190.0691.23798.6
5.61-20120.0651560.9920.0220.071.206100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EGL

6egl


Resolution: 2.08→17.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.964 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.242 125 4.8 %RANDOM
Rwork0.214 ---
obs0.216 2602 99.8 %-
Displacement parametersBiso max: 141.77 Å2 / Biso mean: 58.46 Å2 / Biso min: 35.99 Å2
Baniso -1Baniso -2Baniso -3
1-7.1347 Å20 Å20 Å2
2--7.1347 Å20 Å2
3----14.2693 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.08→17.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms283 0 1 24 308
Biso mean--53.89 56.86 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d123SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes53HARMONIC5
X-RAY DIFFRACTIONt_it299HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion38SEMIHARMONIC5
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_contact358SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d299HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg401HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion25.06
LS refinement shellResolution: 2.08→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4033 18 4.15 %
Rwork0.231 416 -
all0.2372 434 -
obs--99.08 %

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