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- PDB-9xv8: Catalytic domain of N1484 E121S variant -

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Basic information

Entry
Database: PDB / ID: 9xv8
TitleCatalytic domain of N1484 E121S variant
ComponentsLipase
KeywordsHYDROLASE / PET hydrolase
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Cutinase / PET hydrolase-like / : / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesMicromonospora ureilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 26, 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: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5026
Polymers57,1222
Non-polymers3804
Water11,025612
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7533
Polymers28,5611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area9620 Å2
MethodPISA
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7493
Polymers28,5611
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.463, 43.941, 84.151
Angle α, β, γ (deg.)89.97, 90.02, 87.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lipase / C3 cluster PET hydrolase


Mass: 28561.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora ureilytica (bacteria) / Gene: DDE19_30945 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A0A3N9XER1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.26M ammonium sulfate, 0.1M HEPES (pH 7.5)

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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: May 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.63→28.05 Å / Num. obs: 57576 / % possible obs: 95.2 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.9
Reflection shellResolution: 1.63→1.699 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5552 / CC1/2: 0.711

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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: 1.64→28.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 2.507 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22517 2888 5 %RANDOM
Rwork0.17128 ---
obs0.17394 54856 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.776 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0.69 Å20.45 Å2
2---0.64 Å20.06 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.64→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 21 612 4463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0114094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163721
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6495628
X-RAY DIFFRACTIONr_angle_other_deg0.481.5578564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.192530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78610574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02974
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_it0.8821.1282147
X-RAY DIFFRACTIONr_mcbond_other0.8811.1282146
X-RAY DIFFRACTIONr_mcangle_it1.3942.0252710
X-RAY DIFFRACTIONr_mcangle_other1.3942.0252711
X-RAY DIFFRACTIONr_scbond_it1.5281.2961947
X-RAY DIFFRACTIONr_scbond_other1.5281.2981948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2582.3152919
X-RAY DIFFRACTIONr_long_range_B_refined8.5518.655557
X-RAY DIFFRACTIONr_long_range_B_other8.12814.965096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.678 Å
RfactorNum. reflection% reflection
Rfree0.295 195 -
Rwork0.276 3692 -
obs--86.69 %

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