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- PDB-5u9t: The Tris-thiolate Zn(II)S3Cl Binding Site Engineered by D-Cystein... -

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Basic information

Entry
Database: PDB / ID: 5u9t
TitleThe Tris-thiolate Zn(II)S3Cl Binding Site Engineered by D-Cysteine Ligands in de Novo Three-stranded Coiled Coil Environment
ComponentsZn(II)Cl(CoilSer L16(DCY))3 2-
KeywordsDE NOVO PROTEIN / De Novo Three-stranded Coiled Coil / De Novo Design / D-amino Acids in Protein Design / D-Cysteine / Tris-thiolate Zn(II)S3Cl complex
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsRuckthong, L. / Peacock, A.F.A. / 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: Chemistry / Year: 2017
Title: d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils.
Authors: Ruckthong, L. / Peacock, A.F.A. / Pascoe, C.E. / Hemmingsen, L. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zn(II)Cl(CoilSer L16(DCY))3 2-
B: Zn(II)Cl(CoilSer L16(DCY))3 2-
C: Zn(II)Cl(CoilSer L16(DCY))3 2-
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,96327
Polymers9,9783
Non-polymers18,98524
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-238 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.119, 28.977, 43.917
Angle α, β, γ (deg.)90.000, 119.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-113-

NA

21B-103-

NA

31C-106-

ACT

41C-106-

ACT

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Components

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Protein/peptide , 1 types, 3 molecules ABC

#1: Protein/peptide Zn(II)Cl(CoilSer L16(DCY))3 2-


Mass: 3325.850 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 58 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Peptide sample: 13.2 mg/mL peptide, 15 mM Zn(OAc)2, 5mM TRIS buffer pH 8.5 Crystallization well condition: 40% PEG 400, 0.1M Acetate buffer pH 4.6 (final pH 5.4)

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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: Jun 11, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→26.53 Å / Num. obs: 6290 / % possible obs: 96.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.68 Å2 / Rmerge(I) obs: 0.06 / Χ2: 2.333 / Net I/σ(I): 15.2 / Num. measured all: 21879
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.92-1.992.90.2071682184.9
1.99-2.073.30.184193.3
2.07-2.163.50.161198.4
2.16-2.283.70.116199.8
2.28-2.423.70.11100
2.42-2.613.70.085198.9
2.61-2.873.70.076198.9
2.87-3.283.60.07198.9
3.28-4.143.50.052198
4.14-503.20.045195.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H5F

3h5f


Resolution: 1.92→26.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.228 312 4.96 %RANDOM
Rwork0.197 ---
obs0.198 6288 96.7 %-
Displacement parametersBiso max: 85.27 Å2 / Biso mean: 36.87 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.6166 Å20 Å2-10.4653 Å2
2--0.6828 Å20 Å2
3----2.2994 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.92→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 93 34 797
Biso mean--58.25 50.04 -
Num. residues----91
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d378SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes98HARMONIC5
X-RAY DIFFRACTIONt_it752HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion91SEMIHARMONIC5
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_contact908SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d757HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg982HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion3.16
LS refinement shellResolution: 1.92→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.273 77 4.58 %
Rwork0.2 1605 -
all0.204 1682 -
obs--91.91 %

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