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- PDB-9ilo: Crystal structure of CTB10-M4 -

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Basic information

Entry
Database: PDB / ID: 9ilo
TitleCrystal structure of CTB10-M4
ComponentsCTB10
KeywordsBIOSYNTHETIC PROTEIN / Artificial photoenzyme
Function / homologyEthD domain / EthD domain / Dimeric alpha-beta barrel / oxidoreductase activity / CTB10
Function and homology information
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsFu, K. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2021YFC2102700 China
Other privateBK20202002 China
Other privateKYCX20_1812 China
Other governmentKYCX20_1816 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Light-Driven Deracemization by a Designed Photoenzyme.
Authors: Li, M. / Zhang, Y. / Fu, K. / Deng, Z. / Yuan, Z. / Luo, Z. / Rao, Y.
History
DepositionJul 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 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: CTB10
B: CTB10


Theoretical massNumber of molelcules
Total (without water)32,8952
Polymers32,8952
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-33 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.181, 121.186, 160.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

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Components

#1: Protein CTB10


Mass: 16447.676 Da / Num. of mol.: 2 / Mutation: W13F,T107A,S120T,H111L,L124G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora sp. JNU001 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A977K7H6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.47 Å3/Da / Density % sol: 72.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M (NH4)2OAc, 1.9 M (NH4)2SO4, 4% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.21→48.33 Å / Num. obs: 29186 / % possible obs: 98 % / Redundancy: 4.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.059 / Rrim(I) all: 0.128 / Net I/σ(I): 13.46
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 2581 / CC1/2: 0.675 / CC star: 0.898 / Rpim(I) all: 0.463 / Rrim(I) all: 0.867 / % possible all: 88.39

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IKU

9iku


Resolution: 2.21→48.33 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1434 4.92 %RANDOM
Rwork0.1885 ---
obs0.19 29175 97.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 0 183 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072096
X-RAY DIFFRACTIONf_angle_d0.9322831
X-RAY DIFFRACTIONf_dihedral_angle_d6.842299
X-RAY DIFFRACTIONf_chiral_restr0.052305
X-RAY DIFFRACTIONf_plane_restr0.008364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.27821320.23972445X-RAY DIFFRACTION86
2.28-2.380.25011550.24692665X-RAY DIFFRACTION97
2.38-2.480.28321640.22612712X-RAY DIFFRACTION98
2.48-2.610.25371600.20932790X-RAY DIFFRACTION99
2.61-2.780.25081430.21572813X-RAY DIFFRACTION100
2.78-2.990.27081280.20972819X-RAY DIFFRACTION100
2.99-3.290.22951510.19392824X-RAY DIFFRACTION100
3.29-3.770.21061340.16722858X-RAY DIFFRACTION100
3.77-4.750.14871250.14872888X-RAY DIFFRACTION100
4.75-48.330.20841420.18992927X-RAY DIFFRACTION99

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