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- PDB-9de4: Er-Bound Structure of Computationally Designed Homotetramer PW1 -

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Basic information

Entry
Database: PDB / ID: 9de4
TitleEr-Bound Structure of Computationally Designed Homotetramer PW1
ComponentsComputationally designed PW1
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homologyERBIUM (III) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Computationally designed PW1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1163
Polymers11,9141
Non-polymers2032
Water18010
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)48,46512
Polymers47,6544
Non-polymers8118
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 area8450 Å2
ΔGint-90 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.990, 65.990, 38.280
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-

ER3

21A-202-

CL

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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-ER3 / ERBIUM (III) ION


Mass: 167.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Er / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.75 Å3/Da / Density % sol: 29.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% 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: ALS / Beamline: 8.3.1 / Wavelength: 1.48283 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 2, 2024
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48283 Å / Relative weight: 1
ReflectionResolution: 2→46.66 Å / Num. obs: 10887 / % possible obs: 99.54 % / Redundancy: 12.9 % / Biso Wilson estimate: 49.76 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04031 / Rpim(I) all: 0.0116 / Rrim(I) all: 0.04199 / Net I/σ(I): 30.35
Reflection shellResolution: 2→2.071 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.7202 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 1740 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.2083 / Rrim(I) all: 0.7504 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.66 Å / SU ML: 0.2954 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 28.8305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2441 1085 9.99 %
Rwork0.197 9779 -
obs0.2017 10864 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.09 Å2
Refinement stepCycle: LAST / Resolution: 2→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 2 10 802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018819
X-RAY DIFFRACTIONf_angle_d0.37481115
X-RAY DIFFRACTIONf_chiral_restr0.0304143
X-RAY DIFFRACTIONf_plane_restr0.0024147
X-RAY DIFFRACTIONf_dihedral_angle_d27.6537302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.35521340.32441205X-RAY DIFFRACTION98.6
2.09-2.20.32951380.25641219X-RAY DIFFRACTION98.91
2.2-2.340.30251340.24731210X-RAY DIFFRACTION99.41
2.34-2.520.32421420.22511237X-RAY DIFFRACTION99.35
2.52-2.770.29781320.2311220X-RAY DIFFRACTION99.71
2.77-3.170.20911360.22721233X-RAY DIFFRACTION99.85
3.18-3.990.23851310.19211197X-RAY DIFFRACTION99.92
4-46.660.21771380.16541258X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.977384647963.0011948458-2.2783122356410.51880551222.285772553156.778213803960.0836597389911-0.90531410995-1.718079014620.747322386893-0.0465895353584-0.8872746297820.503704014305-0.0704908035801-0.1739127453930.5050190038550.06612303551410.004529308631740.3695555963080.2558034348720.7278311498087.26366528925-18.96947718742.98229601228
25.618045041310.7343861712882.985526115222.86976547791-0.8497411801395.490237327-0.146605657919-0.332501664875-0.1909299341850.561726964996-0.761686937617-1.132882056180.8467170031480.318827022899-0.2388261756350.4369617610050.0433672768328-0.1316171089860.4588485974860.1890351302970.84042757064112.2929186882-14.0016411132-1.64657660354
32.018555989442.781597909315.430471962935.445024477987.208485402592.02183712096-2.39498431599-0.835058325751-4.021813045680.06562614685233.22893249663-0.7291198052581.027113242770.8100050830220.3709387543091.93245772002-0.08210353009460.7963357682891.03084973670.4703743465211.609254284891.31868929206-25.21863917568.37311013823
47.473556310071.25897439705-0.634580491911.9940694335-1.42915693091.695685008630.173054612515-1.15090351722-0.58176181521.05586577868-0.3568176931880.3992168301980.429414260172-0.00796696097788-0.05091212907250.354433525364-0.01015031548030.1668337263930.563230038620.1663816726450.567750130103-2.31157094086-15.35395524554.52452411397
57.046716862430.7684626546230.9505392059658.35669585423-0.6109301576893.03907593979-0.133932166373-0.8715043730510.3076038117820.784953092865-0.2336823492690.0802273611088-0.577526999288-0.4368268373830.4142286603460.446364622485-0.04672844750460.1251253039370.457370629916-0.02305012444210.4023757884191.08649169662-7.544293756681.48329436069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 62 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 14 )
4X-RAY DIFFRACTION4chain 'A' and (resid 15 through 36 )
5X-RAY DIFFRACTION5chain 'A' and (resid 37 through 61 )

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