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- PDB-5kb1: Crystal Structure of a Tris-thiolate Hg(II) Complex in a de Novo ... -

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Basic information

Entry
Database: PDB / ID: 5kb1
TitleCrystal Structure of a Tris-thiolate Hg(II) Complex in a de Novo Three Stranded Coiled Coil Peptide
ComponentsHg(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
KeywordsDE NOVO PROTEIN / Three Stranded Coiled Coil Tris-thiolate Hg(II) Complex in Helical Coiled Coil / De novo Designed Peptide
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRuckcthong, 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_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_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_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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.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_symmetry
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,5075
Polymers4,1401
Non-polymers3674
Water41423
1
A: Hg(II)Zn(II)(GRAND Coil Ser-L16CL30H)3+
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)13,52015
Polymers12,4193
Non-polymers1,10112
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 area4520 Å2
ΔGint-195 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.048, 38.048, 143.651
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-

HG

31A-104-

CL

41A-222-

HOH

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Components

#1: Protein/peptide Hg(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-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#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.: 23 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris buffer pH 8.5, 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 2585 / % possible obs: 99.9 % / Redundancy: 18.2 % / Biso Wilson estimate: 37.16 Å2 / Rmerge(I) obs: 0.094 / Net I/av σ(I): 28.964 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.09-2.1318.20.4831100
2.13-2.1619.20.3921100
2.16-2.2119.60.3611100
2.21-2.2520.50.3471100
2.25-2.319.90.2951100
2.3-2.3519.30.2611100
2.35-2.4119.70.2291100
2.41-2.4820.10.2431100
2.48-2.5519.10.1961100
2.55-2.6319.10.181100
2.63-2.7318.80.1651100
2.73-2.8418.60.1421100
2.84-2.9718.80.1431100
2.97-3.1218.30.129199.2
3.12-3.3217.50.102199.2
3.32-3.5717.20.0911100
3.57-3.9316.40.0831100
3.93-4.515.90.0651100
4.5-5.6715.80.0681100
5.67-5013.60.065199.4

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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: apo-(GRAND Coil Ser L12dLL16C)3

Resolution: 2.09→47.88 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.919 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.257 142 5.5 %RANDOM
Rwork0.218 ---
obs0.22 2584 99.8 %-
Displacement parametersBiso max: 103.96 Å2 / Biso mean: 47.88 Å2 / Biso min: 26.61 Å2
Baniso -1Baniso -2Baniso -3
1-7.8492 Å20 Å20 Å2
2--7.8492 Å20 Å2
3----15.6985 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.09→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms278 0 4 23 305
Biso mean--34.88 48.45 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d116SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes9HARMONIC2
X-RAY DIFFRACTIONt_gen_planes42HARMONIC5
X-RAY DIFFRACTIONt_it296HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion37SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact345SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d296HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg396HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion18.81
LS refinement shellResolution: 2.09→2.34 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.191 36 5.08 %
Rwork0.171 673 -
all-709 -
obs--99.86 %

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