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- PDB-8hqp: Crystal structure of AbHheG mutant from Acidimicrobiia bacterium -

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Basic information

Entry
Database: PDB / ID: 8hqp
TitleCrystal structure of AbHheG mutant from Acidimicrobiia bacterium
ComponentsAbHheG_m
KeywordsOXIDOREDUCTASE / protein / mutant
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: 1.62 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
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
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: AbHheG_m
B: AbHheG_m
C: AbHheG_m
D: AbHheG_m


Theoretical massNumber of molelcules
Total (without water)104,7834
Polymers104,7834
Non-polymers00
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-72 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.247, 87.210, 121.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AbHheG_m


Mass: 26195.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidimicrobiia bacterium (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.1 M 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: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 110244 / % possible obs: 100 % / Redundancy: 14.22 % / CC1/2: 0.99 / CC star: 0.65 / Net I/σ(I): 22.97
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 14.68 % / Mean I/σ(I) obs: 2.85 / Num. unique obs: 8063 / CC1/2: 0.64 / CC star: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WKQ

7wkq


Resolution: 1.62→49.82 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 5364 5.03 %
Rwork0.2072 --
obs0.2084 106734 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 0 792 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.405
X-RAY DIFFRACTIONf_dihedral_angle_d6.749990
X-RAY DIFFRACTIONf_chiral_restr0.1671085
X-RAY DIFFRACTIONf_plane_restr0.0141252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.680.29885530.258610210X-RAY DIFFRACTION99
1.68-1.750.30425230.253810275X-RAY DIFFRACTION99
1.75-1.820.26955610.223310304X-RAY DIFFRACTION100
1.82-1.920.36234600.34389018X-RAY DIFFRACTION87
1.92-2.040.28985430.264610043X-RAY DIFFRACTION97
2.04-2.20.30715420.256810329X-RAY DIFFRACTION99
2.2-2.420.22754970.22279313X-RAY DIFFRACTION89
2.42-2.770.21975620.194510454X-RAY DIFFRACTION100
2.77-3.490.20555540.182810554X-RAY DIFFRACTION100
3.49-49.820.18685690.171410870X-RAY DIFFRACTION100

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