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- PDB-7l33: X-ray Structure of a Cu-Bound De Novo Designed Peptide Trimer -

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Basic information

Entry
Database: PDB / ID: 7l33
TitleX-ray Structure of a Cu-Bound De Novo Designed Peptide Trimer
ComponentsCu-3SCC
KeywordsDE NOVO PROTEIN / Coiled Coil / Copper / Metallopeptide / Artificial Enzymes
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChakraborty, S. / Wawrzak, Z. / Prasad, P. / Mitra, S. / Prakash, D.
CitationJournal: Acs Catalysis / Year: 2021
Title: De Novo Design of a Self-Assembled Artificial Copper Peptide that Activates and Reduces Peroxide
Authors: Mitra, S. / Prakash, D. / Rajabimoghadam, K. / Wawrzak, Z. / Prasad, P. / Wu, T. / Misra, S.K. / Sharp, J.S. / Garcia-Bosch, I. / Chakraborty, S.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cu-3SCC
B: Cu-3SCC
C: Cu-3SCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9676
Polymers9,7763
Non-polymers1913
Water23413
1
A: Cu-3SCC
hetero molecules

A: Cu-3SCC
hetero molecules

A: Cu-3SCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9676
Polymers9,7763
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area3940 Å2
ΔGint-52 kcal/mol
Surface area5940 Å2
MethodPISA
2
B: Cu-3SCC
hetero molecules

B: Cu-3SCC
hetero molecules

B: Cu-3SCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9676
Polymers9,7763
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3480 Å2
ΔGint-53 kcal/mol
Surface area5740 Å2
MethodPISA
3
C: Cu-3SCC
hetero molecules

C: Cu-3SCC
hetero molecules

C: Cu-3SCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9676
Polymers9,7763
Non-polymers1913
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 area3850 Å2
ΔGint-58 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.260, 39.260, 83.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-101-

CU

21B-101-

CU

31C-101-

CU

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 1 or resid 3...
21(chain B and (resid 0 through 1 or resid 3...
31(chain C and (resid 0 through 1 or resid 3...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ACEACEGLYGLY(chain A and (resid 0 through 1 or resid 3...AA0 - 11 - 2
12ALAALAILEILE(chain A and (resid 0 through 1 or resid 3...AA3 - 54 - 6
13LYSLYSLYSLYS(chain A and (resid 0 through 1 or resid 3...AA67
14ACEACEGLYGLY(chain A and (resid 0 through 1 or resid 3...AA0 - 301 - 31
15ACEACEGLYGLY(chain A and (resid 0 through 1 or resid 3...AA0 - 301 - 31
16ACEACEGLYGLY(chain A and (resid 0 through 1 or resid 3...AA0 - 301 - 31
17ACEACEGLYGLY(chain A and (resid 0 through 1 or resid 3...AA0 - 301 - 31
18ACEACEGLYGLY(chain A and (resid 0 through 1 or resid 3...AA0 - 301 - 31
21ACEACEGLYGLY(chain B and (resid 0 through 1 or resid 3...BB0 - 11 - 2
22ALAALAILEILE(chain B and (resid 0 through 1 or resid 3...BB3 - 124 - 13
23LYSLYSLYSLYS(chain B and (resid 0 through 1 or resid 3...BB1314
24ACEACEGLYGLY(chain B and (resid 0 through 1 or resid 3...BB0 - 301 - 31
25ACEACEGLYGLY(chain B and (resid 0 through 1 or resid 3...BB0 - 301 - 31
26ACEACEGLYGLY(chain B and (resid 0 through 1 or resid 3...BB0 - 301 - 31
27ACEACEGLYGLY(chain B and (resid 0 through 1 or resid 3...BB0 - 301 - 31
28ACEACEGLYGLY(chain B and (resid 0 through 1 or resid 3...BB0 - 301 - 31
31ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 11 - 2
32ALAALAILEILE(chain C and (resid 0 through 1 or resid 3...CC3 - 54 - 6
33ACEACEACEACE(chain C and (resid 0 through 1 or resid 3...CC01
34ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 301 - 31
35ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 301 - 31
36ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 301 - 31
37ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 301 - 31
38ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 301 - 31
39ACEACEGLYGLY(chain C and (resid 0 through 1 or resid 3...CC0 - 301 - 31

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Components

#1: Protein/peptide Cu-3SCC


Mass: 3258.809 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2.6H20, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→31.5 Å / Num. obs: 12815 / % possible obs: 98.9 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.031 / Rrim(I) all: 0.102 / Net I/σ(I): 10.2 / Num. measured all: 138001
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.497.23.79161288530.3721.4394.0740.690.8
6.48-31.5100.07415461540.9990.0250.0783098

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZL

4dzl


Resolution: 1.45→20.907 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 48.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2945 554 4.4 %
Rwork0.2687 12029 -
obs0.2698 12583 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.43 Å2 / Biso mean: 40.1871 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 1.45→20.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 3 13 686
Biso mean--84.81 43.89 -
Num. residues----93
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A231X-RAY DIFFRACTION9.217TORSIONAL
12B231X-RAY DIFFRACTION9.217TORSIONAL
13C231X-RAY DIFFRACTION9.217TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.59590.4421290.4256280391
1.5959-1.82670.40161700.354302399
1.8267-2.3010.33271240.3088310099

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