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- PDB-9iwu: CTB10-PE3.0-(R)-1g complex -

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Basic information

Entry
Database: PDB / ID: 9iwu
TitleCTB10-PE3.0-(R)-1g complex
ComponentsCTB10
KeywordsBIOSYNTHETIC PROTEIN / artificial photoenzyme
Function / homologyEthD domain / EthD domain / Dimeric alpha-beta barrel / oxidoreductase activity / : / DI(HYDROXYETHYL)ETHER / CTB10
Function and homology information
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFu, K. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2021YFC2102700 China
Other privateBK20202002 China
Other privateKYCX20_1812 China
Other privateKYCX20_1816 China
CitationJournal: To Be Published
Title: Crystal structure of CTB10-PE3.0-(R)-1g
Authors: Fu, K. / Rao, Y.J.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 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
C: CTB10
D: CTB10
E: CTB10
F: CTB10
G: CTB10
H: CTB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,56218
Polymers132,6548
Non-polymers1,90810
Water5,206289
1
A: CTB10
B: CTB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5244
Polymers33,1632
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-31 kcal/mol
Surface area12420 Å2
MethodPISA
2
C: CTB10
D: CTB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4183
Polymers33,1632
Non-polymers2541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-33 kcal/mol
Surface area11970 Å2
MethodPISA
3
E: CTB10
H: CTB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8566
Polymers33,1632
Non-polymers6934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-34 kcal/mol
Surface area11230 Å2
MethodPISA
4
F: CTB10
G: CTB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7645
Polymers33,1632
Non-polymers6013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-33 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.130, 163.710, 87.408
Angle α, β, γ (deg.)90.00, 93.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CTB10


Mass: 16581.748 Da / Num. of mol.: 8 / Mutation: M40PBF, M86I
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: Chemical
ChemComp-A1EAB / 2-[(3-cyanophenyl)methyl]-5,5-dimethyl-hexa-2,3-dienamide


Mass: 254.327 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H18N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% v/v isopropanol, 0.1 M MES monohydrate pH 6.0, 24% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.2→46.27 Å / Num. obs: 54459 / % possible obs: 97.81 % / Redundancy: 13.2 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1487 / Rpim(I) all: 0.04253 / Rrim(I) all: 0.1548 / Net I/σ(I): 16.69
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 3.41 / Num. unique obs: 5406 / CC1/2: 0.892 / CC star: 0.971 / Rpim(I) all: 0.2589 / Rrim(I) all: 0.9582 / % possible all: 97.26

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IKU

9iku


Resolution: 2.2→46.27 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 2782 5.11 %
Rwork0.1824 --
obs0.1852 54459 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8413 0 13 289 8715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158667
X-RAY DIFFRACTIONf_angle_d1.43911736
X-RAY DIFFRACTIONf_dihedral_angle_d9.1141262
X-RAY DIFFRACTIONf_chiral_restr0.0741254
X-RAY DIFFRACTIONf_plane_restr0.0111493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.34691110.24942520X-RAY DIFFRACTION95
2.24-2.280.31571380.22972591X-RAY DIFFRACTION98
2.28-2.320.31181410.22692571X-RAY DIFFRACTION98
2.32-2.370.34461270.22082562X-RAY DIFFRACTION98
2.37-2.420.26961300.21622549X-RAY DIFFRACTION96
2.42-2.470.31611510.2132565X-RAY DIFFRACTION98
2.47-2.540.29021510.20282528X-RAY DIFFRACTION98
2.54-2.610.29651270.20732658X-RAY DIFFRACTION98
2.61-2.680.29871610.20462523X-RAY DIFFRACTION98
2.68-2.770.2771310.19432627X-RAY DIFFRACTION98
2.77-2.870.2511490.19732558X-RAY DIFFRACTION98
2.87-2.980.26831750.19822536X-RAY DIFFRACTION97
2.98-3.120.25351140.19872615X-RAY DIFFRACTION98
3.12-3.280.25981510.18432618X-RAY DIFFRACTION98
3.28-3.490.22011270.17182614X-RAY DIFFRACTION98
3.49-3.760.20561240.17072605X-RAY DIFFRACTION98
3.76-4.130.20661440.15812583X-RAY DIFFRACTION98
4.13-4.730.16681330.13642635X-RAY DIFFRACTION99
4.73-5.960.21231400.17242610X-RAY DIFFRACTION98
5.96-46.270.20381570.17922609X-RAY DIFFRACTION97

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