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- PDB-5kb0: Crystal Structure of a Tris-thiolate Pb(II) Complex in a de Novo ... -

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Entry
Database: PDB / ID: 5kb0
TitleCrystal Structure of a Tris-thiolate Pb(II) Complex in a de Novo Three-stranded Coiled Coil Peptide
ComponentsPb(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
KeywordsDE NOVO PROTEIN / Three-stranded Coiled Coil Tris-thiolate Pb(II) Complex in de Novo Peptide / De Novo Designed Peptide
Function / homologyLEAD (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsRuckthong, L. / Zastrow, M.L. / Stuckey, J.A. / Pecoraro, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES012236 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Crystallographic Examination of Predisposition versus Preorganization in de Novo Designed Metalloproteins.
Authors: Ruckthong, L. / Zastrow, M.L. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pb(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5135
Polymers4,1401
Non-polymers3734
Water27015
1
A: Pb(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
hetero molecules

A: Pb(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
hetero molecules

A: Pb(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,54015
Polymers12,4193
Non-polymers1,12012
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 area4430 Å2
ΔGint-203 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.117, 38.117, 144.455
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-

ZN

21A-103-

PB

31A-104-

CL

41A-208-

HOH

51A-213-

HOH

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Components

#1: Protein/peptide Pb(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+


Mass: 4139.789 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: MES pH 6.5, PEG-1000 / PH range: 6.5-8.5

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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 24, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 2406 / % possible obs: 99.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.65 Å2 / Rmerge(I) obs: 0.136 / Net I/av σ(I): 9.604 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.13-2.175.80.4461100
2.17-2.215.60.35198.4
2.21-2.255.70.3511100
2.25-2.295.70.3281100
2.29-2.345.60.325198.4
2.34-2.45.40.266199.1
2.4-2.465.80.2821100
2.46-2.535.50.269199.2
2.53-2.65.70.224199.1
2.6-2.685.80.217199.2
2.68-2.785.90.211198.3
2.78-2.895.80.1941100
2.89-3.025.30.16199.1
3.02-3.185.60.1691100
3.18-3.385.60.142198.3
3.38-3.645.60.156199.2
3.64-4.015.50.128199.2
4.01-4.595.60.1091100
4.59-5.785.30.1041100
5.78-504.40.106195.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A peptide strand from Hg(II)Zn(II)(GRAND-CSL16CL30H)3+ structure

Resolution: 2.13→32.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.946 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.237 128 5.32 %RANDOM
Rwork0.206 ---
obs0.208 2405 97.1 %-
Displacement parametersBiso max: 140.03 Å2 / Biso mean: 53.38 Å2 / Biso min: 25.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.9744 Å20 Å20 Å2
2--0.9744 Å20 Å2
3----1.9489 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.13→32.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms289 0 4 16 309
Biso mean--36.8 49.44 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d118SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes10HARMONIC2
X-RAY DIFFRACTIONt_gen_planes40HARMONIC5
X-RAY DIFFRACTIONt_it296HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion36SEMIHARMONIC5
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_contact312SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d296HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg394HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion21.8
LS refinement shellResolution: 2.13→2.38 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.228 33 5.24 %
Rwork0.179 597 -
all-630 -
obs--91.97 %
Refinement TLS params.Method: refined / Origin x: -15.1188 Å / Origin y: 6.9583 Å / Origin z: 13.091 Å
111213212223313233
T-0.065 Å20.0183 Å2-0.0107 Å2--0.0546 Å20.0231 Å2---0.0231 Å2
L2.0139 °20.7085 °2-0.5173 °2-2.8441 °2-2.6791 °2--6.3666 °2
S-0.0608 Å °-0.3358 Å °-0.2066 Å °0.3519 Å °0.0257 Å °-0.0472 Å °-0.0614 Å °-0.0667 Å °0.0351 Å °
Refinement TLS groupSelection details: {A|1 - 36}

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