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- PDB-9bqr: X-ray Structure of a Second-Sphere H-bond Deletion Mutant of a De... -

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Basic information

Entry
Database: PDB / ID: 9bqr
TitleX-ray Structure of a Second-Sphere H-bond Deletion Mutant of a De Novo Designed Self Assembled Peptide Tetramer Featuring a Cu(His)4(H2O) Coordination Motif
ComponentsK6E/E8K Double Mutant of Cu-4SCC
KeywordsDE NOVO PROTEIN / De Novo Design
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsChakraborty, S. / Sony, S. / Prakash, D. / Andi, B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: Controlling outer-sphere solvent reorganization energy to turn on or off the function of artificial metalloenzymes.
Authors: Prakash, D. / Mitra, S. / Sony, S. / Murphy, M. / Andi, B. / Ashley, L. / Prasad, P. / Chakraborty, S.
History
DepositionMay 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: K6E/E8K Double Mutant of Cu-4SCC
B: K6E/E8K Double Mutant of Cu-4SCC
C: K6E/E8K Double Mutant of Cu-4SCC
D: K6E/E8K Double Mutant of Cu-4SCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1185
Polymers16,0554
Non-polymers641
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-67 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.553, 45.309, 40.524
Angle α, β, γ (deg.)90.00, 98.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
K6E/E8K Double Mutant of Cu-4SCC


Mass: 4013.703 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 0.2M MgCl2.6H2O, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.47→28.15 Å / Num. obs: 20743 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.9
Reflection shellResolution: 1.47→1.51 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 1440 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→28.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.639 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 1009 4.9 %RANDOM
Rwork0.20337 ---
obs0.2049 19729 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.232 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.47→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 1 93 1224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161212
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.8181511
X-RAY DIFFRACTIONr_angle_other_deg0.651.7952788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87110232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02211
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5373.076591
X-RAY DIFFRACTIONr_mcbond_other3.4643.07590
X-RAY DIFFRACTIONr_mcangle_it5.2055.459728
X-RAY DIFFRACTIONr_mcangle_other5.2025.46729
X-RAY DIFFRACTIONr_scbond_it4.3713.534543
X-RAY DIFFRACTIONr_scbond_other4.3683.535544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0066.253784
X-RAY DIFFRACTIONr_long_range_B_refined11.71936.121429
X-RAY DIFFRACTIONr_long_range_B_other11.79534.961391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.472→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 70 -
Rwork0.324 1366 -
obs--91.35 %

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