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- PDB-7n2z: Crystal Structure of a de Novo Three-stranded Coiled Coil Peptide... -

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Basic information

Entry
Database: PDB / ID: 7n2z
TitleCrystal Structure of a de Novo Three-stranded Coiled Coil Peptide Containing Trigonal Pyrmidal Pb(II) complexes in the dual Tris-thiolate Site
ComponentsPb(II)2-(GRAND CoilSerL16CL23C)3
KeywordsBIOSYNTHETIC PROTEIN / Three-stranded Coiled Coil / 3SCC / Trigonal Pyramidal Lead Complexes / de Novo Protein / Desinged Protein / Heavy Metal Sites in Protein
Function / homologyLEAD (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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: Pb(II)2-(GRAND CoilSerL16CL23C)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6205
Polymers4,1051
Non-polymers5154
Water1,40578
1
A: Pb(II)2-(GRAND CoilSerL16CL23C)3
hetero molecules

A: Pb(II)2-(GRAND CoilSerL16CL23C)3
hetero molecules

A: Pb(II)2-(GRAND CoilSerL16CL23C)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,86015
Polymers12,3143
Non-polymers1,54612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4470 Å2
ΔGint-124 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.130, 38.130, 139.957
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-

PB

21A-103-

PB

31A-236-

HOH

41A-263-

HOH

51A-276-

HOH

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Components

#1: Protein/peptide Pb(II)2-(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: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Pb / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 40% (v/v) PEG-400, sodium acetate buffer pH 4.5 at a final well solution pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: C(111) / 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: 1.29→50 Å / Num. obs: 10269 / % possible obs: 99.7 % / Redundancy: 15.4 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.016 / Rrim(I) all: 0.063 / Χ2: 1.063 / Net I/σ(I): 10.6 / Num. measured all: 157731
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.29-1.3115.20.5625120.9760.1480.5810.654100
1.31-1.3415.50.5014860.980.1310.5180.672100
1.34-1.3615.70.445170.980.1140.4540.687100
1.36-1.3915.80.3774950.9750.0970.3890.75100
1.39-1.4215.80.3044960.990.0790.3150.772100
1.42-1.4515.70.2445000.9970.0630.2520.809100
1.45-1.49160.1925140.9980.0490.1990.878100
1.49-1.5315.70.1465160.9990.0380.150.903100
1.53-1.5715.70.1555040.9980.040.160.922100
1.57-1.63160.1324990.9970.0340.1360.982100
1.63-1.6815.70.1195120.9970.0310.1231.049100
1.68-1.7515.60.1045170.9980.0270.1081.148100
1.75-1.8315.70.0945140.9980.0250.0971.208100
1.83-1.9315.30.0865050.9970.0230.0891.416100
1.93-2.0515.30.0735170.9990.0190.0761.406100
2.05-2.2115.10.0645220.9990.0170.0661.463100
2.21-2.4315.10.0565200.9990.0150.0581.421100
2.43-2.7814.80.0565340.9990.0150.0571.474100
2.78-3.514.30.0495310.9990.0130.0511.30898.7
3.5-5013.30.055580.9990.0140.0521.37396.2

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Processing

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

6egl


Resolution: 1.29→24.02 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.056 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.172 507 4.94 %RANDOM
Rwork0.164 ---
obs0.164 10267 99.8 %-
Displacement parametersBiso max: 158.65 Å2 / Biso mean: 26.5 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.9376 Å20 Å20 Å2
2---2.9376 Å20 Å2
3---5.8752 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: final / Resolution: 1.29→24.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms285 0 5 78 368
Biso mean--16.1 34.69 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d163SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes73HARMONIC5
X-RAY DIFFRACTIONt_it372HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion47SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact546SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d372HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg514HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion17.96
LS refinement shellResolution: 1.29→1.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.179 21 5.11 %
Rwork0.1842 390 -
all0.184 411 -
obs--100 %

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