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- PDB-9im9: CTB10-M4-(S)-1d complex -

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Basic information

Entry
Database: PDB / ID: 9im9
TitleCTB10-M4-(S)-1d complex
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
DepositionJul 2, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,13212
Polymers32,8952
Non-polymers1,23710
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-75 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.384, 121.402, 160.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-A1D9Q / (3~{S})-1',1'-bis(chloranyl)-5-methyl-spiro[1~{H}-indole-3,2'-cyclopropane]-2-one


Mass: 242.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9Cl2NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 4.93 Å3/Da / Density % sol: 75.04 %
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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.81→48.46 Å / Num. obs: 53676 / % possible obs: 99.73 % / Redundancy: 13.2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07107 / Rpim(I) all: 0.02035 / Rrim(I) all: 0.07398 / Net I/σ(I): 23.32
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.6112 / Mean I/σ(I) obs: 3.71 / Num. unique obs: 5172 / CC1/2: 0.931 / CC star: 0.982 / Rpim(I) all: 0.1767 / Rrim(I) all: 0.6367 / % possible all: 97.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IKU

9iku


Resolution: 1.81→48.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.681 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20092 2709 5 %RANDOM
Rwork0.17993 ---
obs0.181 50967 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.761 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20 Å2
2--0.44 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.81→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 0 198 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122141
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161971
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.8392903
X-RAY DIFFRACTIONr_angle_other_deg0.7391.7744555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.493511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40310369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1480.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
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_it2.4112.283990
X-RAY DIFFRACTIONr_mcbond_other2.412.282990
X-RAY DIFFRACTIONr_mcangle_it3.3524.0871234
X-RAY DIFFRACTIONr_mcangle_other3.3524.0911235
X-RAY DIFFRACTIONr_scbond_it4.3262.9081151
X-RAY DIFFRACTIONr_scbond_other4.3242.911152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4915.1371664
X-RAY DIFFRACTIONr_long_range_B_refined7.90223.732427
X-RAY DIFFRACTIONr_long_range_B_other7.82523.212374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 193 -
Rwork0.284 3624 -
obs--96.88 %

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