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- PDB-8zbc: An acyltransferase with selective perhydrolytic activity -

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Basic information

Entry
Database: PDB / ID: 8zbc
TitleAn acyltransferase with selective perhydrolytic activity
ComponentsSGNH/GDSL hydrolase family protein
KeywordsHYDROLASE / Perhydrolase / Hexmaer / SGNH superfamily
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / carboxylic ester hydrolase activity / SGNH/GDSL hydrolase family protein
Function and homology information
Biological speciesPelagibius litoralis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsYin, Z. / Jing, W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: An acyltransferase with selective perhydrolytic activity
Authors: Yin, Z. / Jing, W.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 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: SGNH/GDSL hydrolase family protein
B: SGNH/GDSL hydrolase family protein
C: SGNH/GDSL hydrolase family protein
D: SGNH/GDSL hydrolase family protein
E: SGNH/GDSL hydrolase family protein
F: SGNH/GDSL hydrolase family protein


Theoretical massNumber of molelcules
Total (without water)150,1696
Polymers150,1696
Non-polymers00
Water00
1
D: SGNH/GDSL hydrolase family protein
E: SGNH/GDSL hydrolase family protein
F: SGNH/GDSL hydrolase family protein

B: SGNH/GDSL hydrolase family protein

A: SGNH/GDSL hydrolase family protein
C: SGNH/GDSL hydrolase family protein


Theoretical massNumber of molelcules
Total (without water)150,1696
Polymers150,1696
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
Buried area11910 Å2
ΔGint-77 kcal/mol
Surface area48700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.750, 165.350, 150.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
SGNH/GDSL hydrolase family protein


Mass: 25028.111 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibius litoralis (bacteria) / Gene: HBA54_08925 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A967CBZ5
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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 60% v/v Tacsimate, 5mM Ethyl acetate, 5mM Hydrogen peroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.45 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.97→48.17 Å / Num. obs: 32663 / % possible obs: 96 % / Redundancy: 3 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 6
Reflection shellResolution: 2.97→3.13 Å / Rmerge(I) obs: 0.418 / Num. unique obs: 12145

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→48.17 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.87 / SU B: 17.788 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1626 5 %RANDOM
Rwork0.20883 ---
obs0.21033 31033 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.992 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0 Å2
2--0.95 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.97→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10071 0 0 0 10071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910347
X-RAY DIFFRACTIONr_bond_other_d0.0010.029749
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.97514211
X-RAY DIFFRACTIONr_angle_other_deg0.806322557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19151330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72324.937397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33151493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6071536
X-RAY DIFFRACTIONr_chiral_restr0.0750.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022049
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_it1.2822.3765338
X-RAY DIFFRACTIONr_mcbond_other1.2792.3765337
X-RAY DIFFRACTIONr_mcangle_it2.1813.5556662
X-RAY DIFFRACTIONr_mcangle_other2.1813.5556663
X-RAY DIFFRACTIONr_scbond_it1.2172.4725009
X-RAY DIFFRACTIONr_scbond_other1.2172.4725010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0893.677550
X-RAY DIFFRACTIONr_long_range_B_refined3.53428.3811342
X-RAY DIFFRACTIONr_long_range_B_other3.53428.38311343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A72310.04
12B72310.04
21A69800.04
22C69800.04
31A72250.05
32D72250.05
41A69740.04
42E69740.04
51A69940.04
52F69940.04
61B69770.04
62C69770.04
71B72060.05
72D72060.05
81B69540.04
82E69540.04
91B69820.04
92F69820.04
101C69760.04
102D69760.04
111C70140.05
112E70140.05
121C70050.05
122F70050.05
131D69790.04
132E69790.04
141D70100.04
142F70100.04
151E69750.05
152F69750.05
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 107 -
Rwork0.313 2330 -
obs--97.91 %

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