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- PDB-9dbv: Cu-Bound Structure of Computationally Designed Homotetramer PW1 -

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Basic information

Entry
Database: PDB / ID: 9dbv
TitleCu-Bound Structure of Computationally Designed Homotetramer PW1
ComponentsComputationally Designed PW1
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoffnagle, A.M. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
CitationJournal: To Be Published
Title: Machine Learning-Guided Design of a Protein Assembly with a Synthetic Metal Center
Authors: Hoffnagle, A.M. / Tsai, C.Y. / Tezcan, F.A.
History
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Computationally Designed PW1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0413
Polymers11,9141
Non-polymers1272
Water81145
1
A: Computationally Designed PW1
hetero molecules

A: Computationally Designed PW1
hetero molecules

A: Computationally Designed PW1
hetero molecules

A: Computationally Designed PW1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,16312
Polymers47,6544
Non-polymers5088
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area8430 Å2
ΔGint-77 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.920, 65.920, 38.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

CU

21A-202-

CU

31A-317-

HOH

41A-329-

HOH

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Components

#1: Protein Computationally Designed PW1


Mass: 11913.565 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.78 Å3/Da / Density % sol: 30.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 23% PEG 3350, 200 mM MgCl2, 100 mM Bis-Tris (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.36242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2023
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36242 Å / Relative weight: 1
ReflectionResolution: 1.8→33.53 Å / Num. obs: 15177 / % possible obs: 99.83 % / Redundancy: 12.8 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06943 / Rpim(I) all: 0.0199 / Rrim(I) all: 0.07229 / Net I/σ(I): 23.02
Reflection shellResolution: 1.8→1.866 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.513 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2387 / CC1/2: 0.79 / CC star: 0.939 / Rpim(I) all: 0.4476 / Rrim(I) all: 1.579 / % possible all: 99.37

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.53 Å / SU ML: 0.2488 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 33.4285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 1513 9.99 %
Rwork0.1855 13625 -
obs0.1905 15138 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 2 45 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067812
X-RAY DIFFRACTIONf_angle_d0.76571103
X-RAY DIFFRACTIONf_chiral_restr0.0553139
X-RAY DIFFRACTIONf_plane_restr0.0071147
X-RAY DIFFRACTIONf_dihedral_angle_d13.6374300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.36141370.31911248X-RAY DIFFRACTION99
1.86-1.930.3321290.29741229X-RAY DIFFRACTION99.78
1.93-20.28811320.26041245X-RAY DIFFRACTION99.49
2-2.090.31981380.21131230X-RAY DIFFRACTION99.85
2.09-2.20.28561400.23271253X-RAY DIFFRACTION99.79
2.21-2.340.26131360.22391225X-RAY DIFFRACTION100
2.34-2.520.23971320.19631253X-RAY DIFFRACTION99.93
2.53-2.780.25221380.19261246X-RAY DIFFRACTION100
2.78-3.180.23931400.19671229X-RAY DIFFRACTION100
3.18-40.19941400.15351232X-RAY DIFFRACTION99.93
4.01-33.530.20911510.15131235X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.1108998732 Å / Origin y: 4.00762902185 Å / Origin z: -20.434268676 Å
111213212223313233
T0.245885751335 Å20.00942220918617 Å2-0.0798795137762 Å2-0.243286819604 Å2-0.0249056138558 Å2--0.295895805035 Å2
L3.55625362462 °20.218836532675 °20.0993413417262 °2-3.95617136856 °2-0.755660712941 °2--2.40295130955 °2
S-0.00279918526006 Å °0.380905920525 Å °0.123630103422 Å °-0.467264084567 Å °-0.0674663640594 Å °0.591583126518 Å °0.00904356624185 Å °-0.0836963028474 Å °0.0646355736714 Å °
Refinement TLS groupSelection details: all

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