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- PDB-9o9w: Crystal structure of an alpha/beta-hydrolase from Actinoplanes sp... -

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Basic information

Entry
Database: PDB / ID: 9o9w
TitleCrystal structure of an alpha/beta-hydrolase from Actinoplanes sp. DH11
Componentspoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET Hydrolase
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesActinoplanes sp. DH11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsNorton-Baker, B. / Storment, O. / Mathews, I.I. / Gauthier, N.P. / McGeehan, J.E. / Beckham, G.T.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
Department of Energy (DOE, United States)DE-SC0022024 United States
Department of Energy (DOE, United States)DE-AC36-08GO28308 United States
CitationJournal: Acs Catalysis / Year: 2025
Title: Machine Learning-Guided Identification of PET Hydrolases from Natural Diversity.
Authors: Norton-Baker, B. / Komp, E. / Gado, J.E. / Denton, M.C.R. / Mathews, I.I. / Murphy, N.P. / Erickson, E. / Storment, O.O. / Sarangi, R. / Gauthier, N.P. / McGeehan, J.E. / Beckham, G.T.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: poly(ethylene terephthalate) hydrolase
B: poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3947
Polymers56,0932
Non-polymers3015
Water8,773487
1
A: poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0872
Polymers28,0471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3085
Polymers28,0471
Non-polymers2614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.250, 87.250, 148.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-579-

HOH

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Components

#1: Protein poly(ethylene terephthalate) hydrolase


Mass: 28046.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes sp. DH11 (bacteria) / Plasmid: pCDB179 / Details (production host): Addgene #91960 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% Precipitant Mix 1, 0.06 M Divalents, Buffer system 1 (pH 6.5) (Morpheus screen)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2024
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.76→37.78 Å / Num. obs: 65654 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.128 / Net I/σ(I): 13.34
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.76-1.812.61447850.6972.7131
1.81-1.861.94847040.8212.0221
1.86-1.911.39145260.911.4441
1.91-1.971.07343970.9351.1141
1.97-2.030.77743190.9620.8081
2.03-2.10.60441570.9740.6281
2.1-2.180.45540090.9840.4741
2.18-2.270.34138420.9860.3561
2.27-2.370.28437220.9930.2951
2.37-2.490.22735720.9950.2351
2.49-2.620.18533910.9960.1921
2.62-2.780.13732020.9970.1421
2.78-2.970.11330260.9980.1181
2.97-3.210.09128410.9980.0941
3.21-3.520.07326210.9980.0761
3.52-3.940.06123670.9980.0641
3.94-4.540.05321140.9990.0561
4.54-5.570.05417980.9990.0561
5.57-7.870.05414370.9990.0561
7.87-37.780.0478240.9980.0491

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→37.78 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.995 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19853 3283 5 %RANDOM
Rwork0.16095 ---
obs0.16278 62371 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å2-0 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 1.76→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 14 487 4353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123979
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163751
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.7845443
X-RAY DIFFRACTIONr_angle_other_deg0.561.7158602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.98536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.46210564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02952
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_it1.8332.3162092
X-RAY DIFFRACTIONr_mcbond_other1.8182.3152092
X-RAY DIFFRACTIONr_mcangle_it2.2394.1522615
X-RAY DIFFRACTIONr_mcangle_other2.2394.1532616
X-RAY DIFFRACTIONr_scbond_it2.8822.5661887
X-RAY DIFFRACTIONr_scbond_other2.8812.5671888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1174.6062829
X-RAY DIFFRACTIONr_long_range_B_refined5.68424.634513
X-RAY DIFFRACTIONr_long_range_B_other5.56123.44396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 239 -
Rwork0.317 4537 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52210.23080.13790.47520.13190.2653-0.0922-0.04640.0381-0.11860.07990.0395-0.0134-0.00210.01230.1521-0.0759-0.02630.06930.00750.015227.071-17.473-3.503
20.15390.032-0.11450.28220.07350.5910.1274-0.02080.00850.0639-0.05270.03250.02550.1031-0.07470.1524-0.0477-0.01370.1449-0.00910.0245.919-41.895-16.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 264
2X-RAY DIFFRACTION2B2 - 259

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