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- PDB-8uqf: Crystal structure of designed cortisol-binding protein hcy129_mpnn5 -

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Entry
Database: PDB / ID: 8uqf
TitleCrystal structure of designed cortisol-binding protein hcy129_mpnn5
Componentsdesigned cortisol-binding protein hcy129_mpnn5
KeywordsDE NOVO PROTEIN / NTF2 / cortisol binding
Function / homologyChem-HCY
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPellock, S.J. / Bera, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Small molecule binding and sensing with a designed protein family
Authors: Lee, G.R. / Pellock, S.J. / Norn, C. / Tischer, D. / Dauparas, J. / Anischenko, I. / Mercer, J.A.M. / Kang, A. / Bera, A. / Nguyen, H. / Goreshnik, I. / Vafeados, D. / Roullier, N. / Han, H. ...Authors: Lee, G.R. / Pellock, S.J. / Norn, C. / Tischer, D. / Dauparas, J. / Anischenko, I. / Mercer, J.A.M. / Kang, A. / Bera, A. / Nguyen, H. / Goreshnik, I. / Vafeados, D. / Roullier, N. / Han, H.L. / Coventry, B. / Liu, D.R. / Yeh, A.H.W.
History
DepositionOct 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed cortisol-binding protein hcy129_mpnn5
B: designed cortisol-binding protein hcy129_mpnn5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6345
Polymers30,8132
Non-polymers8213
Water1,36976
1
A: designed cortisol-binding protein hcy129_mpnn5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7692
Polymers15,4061
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: designed cortisol-binding protein hcy129_mpnn5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8653
Polymers15,4061
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.016, 48.609, 56.438
Angle α, β, γ (deg.)90.000, 93.990, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein designed cortisol-binding protein hcy129_mpnn5


Mass: 15406.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL


Mass: 362.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, hormone*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M ammonium sulfate, 30% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.52→47.9 Å / Num. obs: 59774 / % possible obs: 90.28 % / Redundancy: 2.5 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.0617 / Rpim(I) all: 0.04351 / Rrim(I) all: 0.07593 / Net I/σ(I): 11.73
Reflection shellResolution: 1.52→1.574 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.8317 / Num. unique obs: 3628 / CC1/2: 0.613 / CC star: 0.872 / Rpim(I) all: 0.5868 / Rrim(I) all: 1.024 / % possible all: 91.52

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→47.9 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 3305 5.53 %
Rwork0.2268 56469 -
obs0.2277 59774 76.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.11 Å2
Refinement stepCycle: LAST / Resolution: 1.52→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 57 76 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02372110
X-RAY DIFFRACTIONf_angle_d1.97252859
X-RAY DIFFRACTIONf_chiral_restr0.3318332
X-RAY DIFFRACTIONf_plane_restr0.0103357
X-RAY DIFFRACTIONf_dihedral_angle_d17.8095809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.37341260.34732270X-RAY DIFFRACTION75.87
1.54-1.560.33621270.3332389X-RAY DIFFRACTION75.56
1.56-1.590.30571440.32252349X-RAY DIFFRACTION76.4
1.59-1.610.34051440.3142333X-RAY DIFFRACTION75.36
1.61-1.640.34041440.31552292X-RAY DIFFRACTION76.41
1.64-1.670.34121530.31642424X-RAY DIFFRACTION77.71
1.67-1.70.3191420.29642370X-RAY DIFFRACTION77.36
1.7-1.740.36631670.28992346X-RAY DIFFRACTION76.85
1.74-1.780.2891930.26852348X-RAY DIFFRACTION74.19
1.78-1.820.28151540.26952338X-RAY DIFFRACTION76.14
1.82-1.860.25611230.25152462X-RAY DIFFRACTION79.78
1.86-1.910.24951450.22642477X-RAY DIFFRACTION80.36
1.91-1.970.24611400.242437X-RAY DIFFRACTION78.88
1.97-2.030.27741560.23732373X-RAY DIFFRACTION77.86
2.03-2.110.24991260.23232440X-RAY DIFFRACTION77.38
2.11-2.190.24271410.21712342X-RAY DIFFRACTION76.12
2.19-2.290.27641360.2152349X-RAY DIFFRACTION76.27
2.29-2.410.33271220.22272295X-RAY DIFFRACTION73.82
2.41-2.560.2321370.24132271X-RAY DIFFRACTION73.3
2.56-2.760.24791330.23362354X-RAY DIFFRACTION76.81
2.76-3.040.23861270.22812356X-RAY DIFFRACTION76.05
3.04-3.480.2211300.21012321X-RAY DIFFRACTION74.66
3.48-4.380.19741650.19752245X-RAY DIFFRACTION73.99
4.38-47.90.22371300.20732288X-RAY DIFFRACTION74.01

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