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- PDB-9dbu: Apo Structure of Computationally Designed Homotetramer PW1 -

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Basic information

Entry
Database: PDB / ID: 9dbu
TitleApo Structure of Computationally Designed Homotetramer PW1
ComponentsComputationally Designed PW1
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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


Theoretical massNumber of molelcules
Total (without water)11,9141
Polymers11,9141
Non-polymers00
Water46826
1
A: Computationally Designed PW1

A: Computationally Designed PW1

A: Computationally Designed PW1

A: Computationally Designed PW1


Theoretical massNumber of molelcules
Total (without water)47,6544
Polymers47,6544
Non-polymers00
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 area7910 Å2
ΔGint-40 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.840, 65.840, 37.970
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-224-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 1.73 Å3/Da / Density % sol: 28.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 21% PEG 1500, 200 mM (NH4)2SO4, 100 mM Bis-Tris (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.99184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 1.7→32.92 Å / Num. obs: 17583 / % possible obs: 99.86 % / Redundancy: 13.1 % / Biso Wilson estimate: 35.75 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05809 / Rpim(I) all: 0.0168 / Rrim(I) all: 0.06054 / Net I/σ(I): 22.42
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.423 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 2863 / CC1/2: 0.757 / CC star: 0.928 / Rpim(I) all: 0.4025 / Rrim(I) all: 1.48 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.92 Å / SU ML: 0.3149 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.8124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2393 907 9.99 %
Rwork0.2062 8172 -
obs0.2095 9079 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 0 26 816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039802
X-RAY DIFFRACTIONf_angle_d0.75291090
X-RAY DIFFRACTIONf_chiral_restr0.0472139
X-RAY DIFFRACTIONf_plane_restr0.0035144
X-RAY DIFFRACTIONf_dihedral_angle_d13.3799295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.32531510.32091369X-RAY DIFFRACTION99.67
1.81-1.950.3971470.32021346X-RAY DIFFRACTION99.93
1.95-2.140.30381460.27521347X-RAY DIFFRACTION100
2.14-2.450.26121540.24461360X-RAY DIFFRACTION99.87
2.45-3.080.25591480.22351343X-RAY DIFFRACTION99.93
3.09-32.920.20381610.16691407X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: 3.84788757635 Å / Origin y: -15.1821575473 Å / Origin z: 2.71169454669 Å
111213212223313233
T0.296337734638 Å20.00481909319966 Å20.0377536145849 Å2-0.302432301591 Å20.135543306011 Å2--0.315008959462 Å2
L5.44834229882 °20.0090746900708 °2-0.365963730504 °2-5.80976324203 °2-0.494005122195 °2--3.28387417116 °2
S-0.129937939099 Å °-0.653373843271 Å °-0.843321517434 Å °0.678415359407 Å °-0.0847124712947 Å °-0.273605377918 Å °0.0719234086257 Å °0.057025677922 Å °0.107304669336 Å °
Refinement TLS groupSelection details: all

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