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- PDB-8stb: The structure of abxF, an enzyme catalyzing the formation of the ... -

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Basic information

Entry
Database: PDB / ID: 8stb
TitleThe structure of abxF, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX
ComponentsGlyoxalase
KeywordsBIOSYNTHETIC PROTEIN / Diels-Alderase / biosynthesis / antibiotics / chiral spiroketal
Function / homologyGlyoxalase/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 / Glyoxalase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLuo, Z. / Jia, X. / Yan, X. / Qu, X. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL180100109 Australia
CitationJournal: To Be Published
Title: The crystal structure of abxF, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX.
Authors: Luo, Z. / Jia, X. / Yan, X. / Qu, X. / Kobe, B.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glyoxalase
A: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3467
Polymers47,9912
Non-polymers3545
Water1,72996
1
B: Glyoxalase


Theoretical massNumber of molelcules
Total (without water)23,9961
Polymers23,9961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3506
Polymers23,9961
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.029, 76.029, 166.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-324-

HOH

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Glyoxalase


Mass: 23995.695 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 BL21(DE3) (bacteria) / References: UniProt: A0A2I6B3F9

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Non-polymers , 5 types, 101 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M ammonium sulphate, 0.001 M zinc chloride, and 0.1 M Bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 0.95374 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.22→45.255 Å / Num. obs: 24967 / % possible obs: 98.02 % / Redundancy: 26.5 % / Biso Wilson estimate: 40.45 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1897 / Rpim(I) all: 0.03794 / Rrim(I) all: 0.1936 / Net I/σ(I): 13.25
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 27 % / Rmerge(I) obs: 0.4371 / Num. unique obs: 2294 / CC1/2: 0.978 / CC star: 0.994 / Rpim(I) all: 0.0845 / Rrim(I) all: 0.4453 / % possible all: 93.79

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→45.18 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 2380 9.72 %
Rwork0.201 --
obs0.2043 24495 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 14 96 3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.456
X-RAY DIFFRACTIONf_dihedral_angle_d5.488465
X-RAY DIFFRACTIONf_chiral_restr0.124481
X-RAY DIFFRACTIONf_plane_restr0.014581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.27131300.19691212X-RAY DIFFRACTION94
2.27-2.310.26281380.19571217X-RAY DIFFRACTION95
2.31-2.370.22141460.19181231X-RAY DIFFRACTION96
2.37-2.430.21711410.19611253X-RAY DIFFRACTION96
2.43-2.490.30131300.22961262X-RAY DIFFRACTION97
2.49-2.570.30871340.22341282X-RAY DIFFRACTION98
2.57-2.650.28171210.19771294X-RAY DIFFRACTION98
2.65-2.740.23351360.19631288X-RAY DIFFRACTION99
2.74-2.850.25191320.20111290X-RAY DIFFRACTION98
2.85-2.980.24861340.2271314X-RAY DIFFRACTION99
2.98-3.140.32451350.24771309X-RAY DIFFRACTION99
3.14-3.340.23371410.2121319X-RAY DIFFRACTION99
3.34-3.60.24321230.19761347X-RAY DIFFRACTION100
3.6-3.960.24321460.1871339X-RAY DIFFRACTION100
3.96-4.530.16121510.16391337X-RAY DIFFRACTION100
4.53-5.70.19541570.17711370X-RAY DIFFRACTION100
5.71-45.180.25771850.23561451X-RAY DIFFRACTION100
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)
12.7653-0.4578-0.44151.0184-0.12511.3135-00.12420.4422-0.09270.02910.2478-0.115-0.11920.02110.31050.0417-0.03320.36140.08810.2732.9005-11.174411.2061
24.47420.677-0.66292.7302-0.21111.0921-0.1677-0.06770.11990.16780.1306-0.0573-0.05890.01670.00750.24790.0417-0.04010.31640.01040.188712.6646-15.289917.2157
33.5118-0.22860.16573.36480.20522.95820.0006-0.0885-0.66850.11260.012-0.44760.24670.5649-0.09570.24620.0777-0.07420.4496-0.00860.436615.6095-24.8721-11.1604
42.74710.66080.3392.4227-0.04292.2662-0.01440.2218-0.231-0.22080.0408-0.11520.02870.2903-0.05060.24280.05650.01530.3415-0.02720.26178.0755-19.7026-18.8118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 11 through 96 )
2X-RAY DIFFRACTION2chain 'B' and (resid 97 through 244 )
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 244 )

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