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- PDB-8h8y: Crystal structure of AbHheG from Acidimicrobiia bacterium -

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Basic information

Entry
Database: PDB / ID: 8h8y
TitleCrystal structure of AbHheG from Acidimicrobiia bacterium
Componentsalpha/beta hydrolase
KeywordsOXIDOREDUCTASE / catalysis
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesAcidimicrobiia bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhou, C.H. / Chen, X. / Han, X. / Liu, W.D. / Wu, Q.Q. / Zhu, D.M. / Ma, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2023
Title: Flipping the Substrate Creates a Highly Selective Halohydrin Dehalogenase for the Synthesis of Chiral 4-Aryl-2-oxazolidinones from Readily Available Epoxides
Authors: Zhou, C. / Chen, X. / Lv, T. / Han, X. / Feng, J. / Liu, W. / Wu, Q. / Zhu, D.
History
DepositionOct 24, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha/beta hydrolase
B: alpha/beta hydrolase
C: alpha/beta hydrolase
D: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2957
Polymers105,0194
Non-polymers2763
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-87 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.887, 62.407, 71.415
Angle α, β, γ (deg.)69.240, 82.880, 62.190
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
alpha/beta hydrolase


Mass: 26254.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidimicrobiia bacterium (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1 Bis-Tris pH 6.5, 2% v/v Tacsimate pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2022
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→52.01 Å / Num. obs: 120656 / % possible obs: 95.7 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.035 / Rrim(I) all: 0.06 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.632.70.3446384173930.9050.2480.4232.494.4
4.9-51.952.40.036918738050.9930.0280.04614.395.2

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WKQ

7wkq


Resolution: 1.55→52.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.012 / SU ML: 0.07 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 5949 4.9 %RANDOM
Rwork0.1717 ---
obs0.1731 114706 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.94 Å2 / Biso mean: 20.294 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å21.12 Å20.86 Å2
2--0.11 Å20.49 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 1.55→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7328 0 18 736 8082
Biso mean--29.62 29.49 -
Num. residues----979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137487
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157083
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.64310161
X-RAY DIFFRACTIONr_angle_other_deg1.511.57116227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54420.722388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.878151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1281568
X-RAY DIFFRACTIONr_chiral_restr0.0760.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021807
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 419 -
Rwork0.243 8373 -
all-8792 -
obs--94.16 %

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