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- PDB-9dbw: Rh-Bound Structure of Computationally Designed Homotetramer PW1 -

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Basic information

Entry
Database: PDB / ID: 9dbw
TitleRh-Bound Structure of Computationally Designed Homotetramer PW1
ComponentsComputationally Designed PW1
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homologyRhodium
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: Computationally Designed PW1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1193
Polymers11,9141
Non-polymers2062
Water27015
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)48,47812
Polymers47,6544
Non-polymers8238
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
Unit cell
Length a, b, c (Å)63.150, 63.150, 37.600
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-

RH

21A-202-

RH

31A-310-

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-RH / Rhodium


Mass: 102.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rh / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 200 mM NaCl, 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: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36242 Å / Relative weight: 1
ReflectionResolution: 2.1→44.65 Å / Num. obs: 8511 / % possible obs: 99.91 % / Redundancy: 12.8 % / Biso Wilson estimate: 45.21 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1039 / Rpim(I) all: 0.0304 / Rrim(I) all: 0.1083 / Net I/σ(I): 13.43
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 1369 / CC1/2: 0.796 / CC star: 0.942 / Rpim(I) all: 0.4047 / Rrim(I) all: 1.423 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.65 Å / SU ML: 0.2769 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 851 10.03 %
Rwork0.189 7633 -
obs0.1959 8484 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 2 15 815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035839
X-RAY DIFFRACTIONf_angle_d0.57271145
X-RAY DIFFRACTIONf_chiral_restr0.0367145
X-RAY DIFFRACTIONf_plane_restr0.0042153
X-RAY DIFFRACTIONf_dihedral_angle_d25.8154312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.32781460.27121267X-RAY DIFFRACTION99.93
2.23-2.40.36861350.24651288X-RAY DIFFRACTION99.86
2.4-2.640.38811560.21721247X-RAY DIFFRACTION99.79
2.65-3.030.26971390.21571277X-RAY DIFFRACTION99.93
3.03-3.820.27791420.20341264X-RAY DIFFRACTION99.79
3.82-44.650.20091330.15281290X-RAY DIFFRACTION99.86
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)
16.36036956175-0.6342852009041.370247179426.12976774963-1.125685254037.54840217347-0.1029071870830.35511545289-0.389175580947-0.0866607296221-0.4994030329340.1727596447270.9239566673150.3960502220260.4970321987530.344719519450.02310962983540.09059787181450.4419107721550.05064496457580.5867768133981.86052164728-18.012815174714.4682950918
27.09162986452.065143876342.678682623276.510263261960.7933962764853.19504158905-0.09577644878450.452857383369-0.310097162799-0.417690142580.301367531422-0.134480896473-0.9060485786670.2850824792620.3594129303380.323910534979-0.004448901995810.01189781292910.2862687028660.002294351338520.431200024527-4.42447596284-7.7794931968512.5013904843
35.77963211072-1.009101358053.567893927345.284052433590.5573330838636.57216091324-0.00792416107023-0.130221179926-0.389141698432-0.387652740990.08105561834450.457229620780.0739327724979-0.0514331217738-0.1760527879390.260258852312-0.07406155589970.01626800271250.2482443168450.05901457578820.454362974903-9.21516879641-16.589038923918.4376305788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 107 )

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