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- PDB-9cte: De novo design of protein catalysts for new-to-nature reactions -

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Basic information

Entry
Database: PDB / ID: 9cte
TitleDe novo design of protein catalysts for new-to-nature reactions
ComponentsDe novo protein
KeywordsDE NOVO PROTEIN / metalloproteins
Function / homology5,15-Diphenylporphyrin containing FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHou, K. / DeGrado, W.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2025
Title: De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts.
Authors: Hou, K. / Huang, W. / Qi, M. / Tugwell, T.H. / Alturaifi, T.M. / Chen, Y. / Zhang, X. / Lu, L. / Mann, S.I. / Liu, P. / Yang, Y. / DeGrado, W.F.
History
DepositionJul 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8165
Polymers15,1941
Non-polymers6234
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.273, 71.273, 114.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein De novo protein


Mass: 15193.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-WUP / 5,15-Diphenylporphyrin containing FE


Mass: 516.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H20FeN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris HCl pH 8.5 and 2.0M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.255→60.57 Å / Num. obs: 7287 / % possible obs: 99.78 % / Redundancy: 2 % / Biso Wilson estimate: 39.65 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.148 / Χ2: 0.96 / Net I/σ(I): 7
Reflection shellResolution: 2.255→2.33 Å / Num. unique obs: 698 / CC1/2: 0.311

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→60.57 Å / SU ML: 0.3703 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2783 729 10 %
Rwork0.2316 6558 -
obs0.2364 7287 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.89 Å2
Refinement stepCycle: LAST / Resolution: 2.26→60.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 40 17 958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193956
X-RAY DIFFRACTIONf_angle_d1.38121295
X-RAY DIFFRACTIONf_chiral_restr0.0427133
X-RAY DIFFRACTIONf_plane_restr0.0206173
X-RAY DIFFRACTIONf_dihedral_angle_d24.3109369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.430.41241400.33861263X-RAY DIFFRACTION99.36
2.43-2.670.33471440.29531287X-RAY DIFFRACTION100
2.67-3.060.31521440.25511302X-RAY DIFFRACTION99.86
3.06-3.850.2721450.20721310X-RAY DIFFRACTION99.86
3.86-60.570.23531560.20391396X-RAY DIFFRACTION99.87

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