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- PDB-9iku: Crystal structure of Se-Met CTB10 -

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Basic information

Entry
Database: PDB / ID: 9iku
TitleCrystal structure of Se-Met CTB10
ComponentsCTB10
KeywordsBIOSYNTHETIC PROTEIN / presumable molecular container
Function / homologyEthD domain / EthD domain / Dimeric alpha-beta barrel / oxidoreductase activity / CTB10
Function and homology information
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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: 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
DepositionJun 29, 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
C: CTB10
D: CTB10
E: CTB10
F: CTB10
G: CTB10
H: CTB10


Theoretical massNumber of molelcules
Total (without water)134,4648
Polymers134,4648
Non-polymers00
Water1,24369
1
A: CTB10
G: CTB10


Theoretical massNumber of molelcules
Total (without water)33,6162
Polymers33,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-29 kcal/mol
Surface area12410 Å2
MethodPISA
2
B: CTB10
F: CTB10


Theoretical massNumber of molelcules
Total (without water)33,6162
Polymers33,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-31 kcal/mol
Surface area11860 Å2
MethodPISA
3
C: CTB10
H: CTB10


Theoretical massNumber of molelcules
Total (without water)33,6162
Polymers33,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-26 kcal/mol
Surface area11930 Å2
MethodPISA
4
D: CTB10
E: CTB10


Theoretical massNumber of molelcules
Total (without water)33,6162
Polymers33,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-31 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.890, 87.740, 85.880
Angle α, β, γ (deg.)90.00, 116.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CTB10


Mass: 16807.969 Da / Num. of mol.: 8
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.: 69 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 18% isopropanol, 0.1 M sodium citrate tribasic dehydrate pH 5.5, 24%(W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→57.72 Å / Num. obs: 47668 / % possible obs: 98.61 % / Redundancy: 6.8 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Χ2: 0.97 / Net I/σ(I): 17.43
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.9163 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 4790 / CC1/2: 0.803 / CC star: 0.944 / Rpim(I) all: 0.3681 / Rrim(I) all: 0.9887 / Χ2: 0.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→57.72 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.75 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25614 2474 5.2 %RANDOM
Rwork0.19072 ---
obs0.19401 45193 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.754 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å2-0 Å2-0.57 Å2
2---0.88 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 2.3→57.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8103 0 0 69 8172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128333
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167486
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.66511276
X-RAY DIFFRACTIONr_angle_other_deg0.5311.57417515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7875989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.079529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.849101346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021628
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1135.5343980
X-RAY DIFFRACTIONr_mcbond_other5.1125.5333980
X-RAY DIFFRACTIONr_mcangle_it7.0258.3034961
X-RAY DIFFRACTIONr_mcangle_other7.0248.3044962
X-RAY DIFFRACTIONr_scbond_it5.7135.9994353
X-RAY DIFFRACTIONr_scbond_other5.7135.9994354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9738.7836316
X-RAY DIFFRACTIONr_long_range_B_refined9.76770.4518994
X-RAY DIFFRACTIONr_long_range_B_other9.76770.4488994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 186 -
Rwork0.31 3348 -
obs--99.47 %

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