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- PDB-5kay: Structure of Spelter bound to Zn2+ -

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Basic information

Entry
Database: PDB / ID: 5kay
TitleStructure of Spelter bound to Zn2+
ComponentsSpelter
KeywordsDE NOVO PROTEIN / Metalloprotein / designed protein
Function / homologyf41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGuffy, S.L. / Der, B.S. / Kuhlman, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117968 United States
National Science Foundation (NSF, United States)CBET-1403663 United States
Citation
Journal: Protein Eng.Des.Sel. / Year: 2016
Title: Probing the minimal determinants of zinc binding with computational protein design.
Authors: Guffy, S.L. / Der, B.S. / Kuhlman, B.
#1: Journal: Proteins / Year: 2013
Title: Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding.
Authors: Der, B.S. / Jha, R.K. / Lewis, S.M. / Thompson, P.M. / Guntas, G. / Kuhlman, B.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 6, 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 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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: Spelter
B: Spelter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5896
Polymers43,4122
Non-polymers1774
Water2,954164
1
A: Spelter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7943
Polymers21,7061
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spelter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7943
Polymers21,7061
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.714, 41.496, 61.506
Angle α, β, γ (deg.)87.270, 83.090, 79.460
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Spelter


Mass: 21706.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pQE-80L
Details (production host): N-terminal MBP+6-His tag with TEV cleavage site; Ampicillin resistance
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG3350 0.22 M sodium iodide 10 mM ammonium acetate

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Data collection

DiffractionMean temperature: 228 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→40.79 Å / Num. obs: 37095 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.823.30.9711.9194
1.82-1.833.30.9382195.4
1.83-1.853.40.8292.3194.8
1.85-1.863.50.92.4196.1
1.86-1.883.60.7742.7195.4
1.88-1.93.70.763195.9
1.9-1.923.80.63.7196.8
1.92-1.943.80.5784195.5
1.94-1.963.90.4894.7197
1.96-1.983.90.4445.1196
1.98-23.90.4155.7196.3
2-2.033.90.4215.8196.8
2.03-2.053.90.3646.6196.3
2.05-2.083.90.2978.1196.9
2.08-2.113.90.2818.5196.4
2.11-2.133.90.2539.5196.9
2.13-2.163.90.2489.6196.8
2.16-2.23.90.21510.8197.2
2.2-2.233.90.19612197.3
2.23-2.273.90.18113.3196.9
2.27-2.313.90.16614.4197.7
2.31-2.353.90.15214.7197
2.35-2.393.90.13816.5197.6
2.39-2.443.90.13317.5197.8
2.44-2.53.90.12518.7197.4
2.5-2.553.90.11420198.1
2.55-2.623.90.10721.4197.9
2.62-2.693.90.10521.7197.8
2.69-2.773.90.09523.5198.1
2.77-2.863.90.08825198.1
2.86-2.963.90.07929.5198.2
2.96-3.083.90.07431.4198.2
3.08-3.223.90.06732.9198.6
3.22-3.393.90.06238.1198.6
3.39-3.63.90.05640.7198.5
3.6-3.883.90.05144.2198.9
3.88-4.273.90.04845.5199
4.27-4.883.80.04846.2199.2
4.88-6.153.80.05244.2199.4
6.15-40.793.80.04250.2199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / Matrix type: sparse / SU B: 2.576 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.133 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1818 5.1 %RANDOM
Rwork0.1928 ---
obs0.1948 33820 79.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.89 Å2 / Biso mean: 25.249 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 4 164 3183
Biso mean--34 27.82 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193068
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9494169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465.025404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.61226140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.781512
X-RAY DIFFRACTIONr_chiral_restr0.1440.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022320
X-RAY DIFFRACTIONr_mcbond_it2.4692.3071606
X-RAY DIFFRACTIONr_mcangle_it3.4183.442005
X-RAY DIFFRACTIONr_scbond_it4.012.6791462

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