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- PDB-9jt3: Crystal structure of AbxF -

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Basic information

Entry
Database: PDB / ID: 9jt3
TitleCrystal structure of AbxF
ComponentsGlyoxalase
KeywordsLYASE / Diels Alder reaction
Function / homology: / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / metal ion binding / Glyoxalase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, M.J. / Kong, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Crystal structure of AbxF
Authors: Yan, X.L. / Qu, X.D. / Zhang, M.J. / Kong, X.D.
History
DepositionOct 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase
B: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2543
Polymers54,1622
Non-polymers921
Water3,927218
1
A: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1732
Polymers27,0811
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glyoxalase


Theoretical massNumber of molelcules
Total (without water)27,0811
Polymers27,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.883, 75.883, 166.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glyoxalase / Enzyme for Diels-Alder reaction


Mass: 27081.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: abxF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I6B3F9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: NaCl, Bistris, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2→83.06 Å / Num. obs: 33722 / % possible obs: 100 % / Redundancy: 21.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.018 / Rrim(I) all: 0.087 / Χ2: 0.95 / Net I/σ(I): 21 / Num. measured all: 723962
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.433 / Num. measured all: 37600 / Num. unique obs: 2434 / CC1/2: 0.965 / Rpim(I) all: 0.113 / Rrim(I) all: 0.447 / Χ2: 0.77 / Net I/σ(I) obs: 6.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.02 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1993 5.94 %
Rwork0.1939 --
obs0.1961 33571 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→56.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 6 218 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073219
X-RAY DIFFRACTIONf_angle_d0.8664389
X-RAY DIFFRACTIONf_dihedral_angle_d5.378463
X-RAY DIFFRACTIONf_chiral_restr0.052476
X-RAY DIFFRACTIONf_plane_restr0.009579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24971400.21852210X-RAY DIFFRACTION100
2.05-2.110.26041400.20622212X-RAY DIFFRACTION100
2.11-2.170.29531390.20612207X-RAY DIFFRACTION100
2.17-2.240.25721410.1992231X-RAY DIFFRACTION100
2.24-2.320.26051390.20192198X-RAY DIFFRACTION100
2.32-2.410.27951390.19942214X-RAY DIFFRACTION100
2.41-2.520.25841420.19892234X-RAY DIFFRACTION100
2.52-2.650.2381410.20132234X-RAY DIFFRACTION100
2.65-2.820.30041420.21722265X-RAY DIFFRACTION100
2.82-3.040.23491420.21312252X-RAY DIFFRACTION100
3.04-3.340.23871390.19562251X-RAY DIFFRACTION100
3.34-3.830.22561460.18222295X-RAY DIFFRACTION100
3.83-4.820.17461470.16762319X-RAY DIFFRACTION100
4.82-56.020.21981560.1992456X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.1186 Å / Origin y: -20.3481 Å / Origin z: -0.3298 Å
111213212223313233
T0.1766 Å20.0005 Å20.0163 Å2-0.2065 Å2-0.0193 Å2--0.2557 Å2
L0.5833 °2-0.0332 °2-0.3645 °2-0.2682 °20.0843 °2--1.1819 °2
S-0.0172 Å °0.0047 Å °0.128 Å °0.0263 Å °0.0124 Å °0.0118 Å °0.0327 Å °-0.1204 Å °-0.003 Å °
Refinement TLS groupSelection details: all

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