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- PDB-6egp: Crystal Structure of a Trigonal Pyramidal Pb(II)S3 Complex in a T... -

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Basic information

Entry
Database: PDB / ID: 6egp
TitleCrystal Structure of a Trigonal Pyramidal Pb(II)S3 Complex in a Three-stranded Coiled coil Peptide
ComponentsPb(II)(GRAND CoilSerL12AL16C)3-
KeywordsDE NOVO PROTEIN / De Novo Three-stranded Coiled Coil Peptide / Trigonal Pyramidal Pb(II)S3 / Tris-thiolate / Metalloprotein
Function / homologyLEAD (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 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: To Be Published
Title: Crystal Structure of a Trigonal Pyramidal Pb(II)S3 Complex in a Three-stranded Coiled coil Peptide
Authors: Ruckthong, L. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,3453
Polymers4,0731
Non-polymers2732
Water1,09961
1
A: Pb(II)(GRAND CoilSerL12AL16C)3-
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)13,0369
Polymers12,2183
Non-polymers8186
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 area4120 Å2
ΔGint-112 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.726, 37.726, 140.042
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-225-

HOH

31A-233-

HOH

41A-257-

HOH

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Components

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


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% v/v PEG3350, 0.2 M sodium acetate

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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: Apr 1, 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: 1.77→50 Å / Num. obs: 4012 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 24.94 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.056 / Rrim(I) all: 0.151 / Χ2: 1.04 / Net I/av σ(I): 16.212 / Net I/σ(I): 7.9 / Num. measured all: 34544
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.88.10.4770.9480.1760.510.634100
1.8-1.8390.4140.9810.1460.440.624100
1.83-1.879.20.4020.9870.140.4260.652100
1.87-1.919.40.3760.9840.1290.3980.68899.5
1.91-1.959.40.3690.9730.1280.3910.69899.5
1.95-1.999.60.2940.980.1010.3110.823100
1.99-2.049.50.3010.9810.1040.3190.88499.5
2.04-2.19.50.2630.9820.0930.280.894100
2.1-2.169.40.2230.9760.0790.2370.97799.5
2.16-2.239.40.2170.990.0790.2321.014100
2.23-2.319.10.1920.9870.0690.2051.07100
2.31-2.48.90.1650.9890.0610.1761.20599.5
2.4-2.518.80.1620.9880.060.1731.178100
2.51-2.648.70.1420.9860.0540.1521.106100
2.64-2.818.50.1360.9920.050.1451.21299.5
2.81-3.0380.130.9910.0510.141.341100
3.03-3.337.80.110.990.0440.1191.32699.5
3.33-3.817.30.1130.9850.0480.1231.57598.6
3.81-4.87.10.1030.9920.0430.1121.34799.5
4.8-5060.1190.990.0560.1332.07493.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6EGL

6egl


Resolution: 1.77→29.61 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.208 203 5.09 %RANDOM
Rwork0.184 ---
obs0.185 3990 99.4 %-
Displacement parametersBiso max: 77.34 Å2 / Biso mean: 28.61 Å2 / Biso min: 15.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.5699 Å20 Å20 Å2
2---3.5699 Å20 Å2
3---7.1397 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.77→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms276 0 2 61 339
Biso mean--21.76 34.8 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d119SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes10HARMONIC2
X-RAY DIFFRACTIONt_gen_planes43HARMONIC5
X-RAY DIFFRACTIONt_it300HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
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_contact449SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d300HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg405HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion1.76
X-RAY DIFFRACTIONt_other_torsion18.49
LS refinement shellResolution: 1.77→1.98 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.197 51 4.59 %
Rwork0.166 1060 -
all-1111 -
obs--99.82 %

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