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- PDB-30zt: PurH inhibited by PMSF -

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Basic information

Entry
Database: PDB / ID: 30zt
TitlePurH inhibited by PMSF
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / inhibitor / alpha beta hydrolase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / phenylmethanesulfonic acid / Dienelactone hydrolase
Function and homology information
Biological speciesAeromicrobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.125 Å
AuthorsBloch, Y. / Panneerselvam, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
Citation
Journal: To Be Published
Title: Observation of sulfonylation elimination products by crystallography
Authors: Bloch, Y. / Panneerselvam, S.
#1: Journal: To Be Published
Title: Discovery of a polyester polyurethane-degrading bacterium from a coastal mudflat and identification of its degrading enzyme.
Authors: Zhang, L. / Cao, K. / Liu, H. / Wang, Y. / Zhang, B. / Han, H. / Cui, Z. / Cao, H.
History
DepositionMay 19, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7373
Polymers29,5421
Non-polymers1952
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-10 kcal/mol
Surface area10560 Å2
Unit cell
Length a, b, c (Å)36.213, 76.054, 82.187
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha/beta hydrolase / Dienelactone hydrolase


Mass: 29541.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromicrobium (bacteria) / Strain: LTX1 / Gene: BJ975_002808, IDH50_06695 / Plasmid: pET derived / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: A0A8I0FTC2
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% (w/v) PEG 3350, 100 mM Glycine pH 9, 7 mM PMSF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.05965 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05965 Å / Relative weight: 1
ReflectionResolution: 1.125→55.82 Å / Num. obs: 86578 / % possible obs: 99.62 % / Redundancy: 23.4 % / Biso Wilson estimate: 10.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.021 / Rrim(I) all: 0.106 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.05-55.89250.04273.6468010.0080.043100
1.125-1.149.61.2380.739660.5790.4071.30893.23

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
DIALS3.23.0-g7aff524e7-releasedata reduction
DIALS3.23.0-g7aff524e7-releasedata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.125→55.82 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.978 / SU R Cruickshank DPI: 0.032 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.032 / SU Rfree Blow DPI: 0.034 / SU Rfree Cruickshank DPI: 0.032
RfactorNum. reflection% reflectionSelection details
Rfree0.1697 1922 -RANDOM
Rwork0.1463 ---
obs0.1468 86359 99.4 %-
Displacement parametersBiso mean: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.5952 Å20 Å20 Å2
2---0.5458 Å20 Å2
3---1.141 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.125→55.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 11 309 2333
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0144360HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.947868HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d1327SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes741HARMONIC5
X-RAY DIFFRACTIONt_it4331HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies18HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4620SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.91
X-RAY DIFFRACTIONt_other_torsion13.79
LS refinement shellResolution: 1.125→1.13 Å
RfactorNum. reflection% reflection
Rfree0.3226 37 -
Rwork0.3166 --
obs--89.78 %

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