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- PDB-9xv7: Catalytic domain of N1356 -

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Basic information

Entry
Database: PDB / ID: 9xv7
TitleCatalytic domain of N1356
ComponentsC3 cluster PET hydrolase
KeywordsHYDROLASE / PET hydrolase
Biological speciesSaccharothrix sp. CB00851 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHwang, H. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
Other governmentRS-2025-10702985
Other governmentRS-2025-06082970
National Research Foundation (NRF, Korea)RS-2024-00439872 Korea, Republic Of
Other governmentP0028353
CitationJournal: J Hazard Mater / Year: 2026
Title: Effect of surface electrostatic potential on pH-activity profile in PET depolymerases.
Authors: Seo, H. / Hwang, H. / Park, J. / Ki, D. / Choi, W. / Yoon, Y. / Kim, D. / Kim, K.J.
History
DepositionNov 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C3 cluster PET hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9166
Polymers28,4861
Non-polymers4305
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint0 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.057, 78.090, 40.222
Angle α, β, γ (deg.)90.00, 113.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C3 cluster PET hydrolase


Mass: 28485.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix sp. CB00851 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) PEG 3350, 0.04M citric acid, 0.06M Bis-Tris propane (pH 6.4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.2→33.68 Å / Num. obs: 69717 / % possible obs: 98.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.9
Reflection shellResolution: 1.2→1.243 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 6464 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→33.68 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.431 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15109 3572 5.1 %RANDOM
Rwork0.13934 ---
obs0.13995 66310 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.48 Å2
2--0.55 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.2→33.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 28 303 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0112097
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161907
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.652864
X-RAY DIFFRACTIONr_angle_other_deg0.6671.5624391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.502513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40210296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
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_it0.8290.7621079
X-RAY DIFFRACTIONr_mcbond_other0.8270.7611078
X-RAY DIFFRACTIONr_mcangle_it1.1691.3771361
X-RAY DIFFRACTIONr_mcangle_other1.1681.3771362
X-RAY DIFFRACTIONr_scbond_it2.021.6061018
X-RAY DIFFRACTIONr_scbond_other2.0261.6441019
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.732.5171504
X-RAY DIFFRACTIONr_long_range_B_refined65.772603
X-RAY DIFFRACTIONr_long_range_B_other66.182603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.229 Å
RfactorNum. reflection% reflection
Rfree0.204 249 -
Rwork0.196 4267 -
obs--86.46 %

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