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- PDB-9qbx: Crystal structure of an atypical fungal aspartate/glutamate racem... -

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Basic information

Entry
Database: PDB / ID: 9qbx
TitleCrystal structure of an atypical fungal aspartate/glutamate racemase family member OpaE
ComponentsEpimerase opaE
KeywordsISOMERASE / Opaen / Asp/Glu racemase superfamily / Epimerase / Stereochemical inversion / Nonribosomal peptide biosynthesis
Function / homologyIsomerases; Racemases and epimerases / : / amino-acid racemase activity / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Epimerase opaE
Function and homology information
Biological speciesAspergillus ustus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZheng, X. / Zheng, L. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: A Novel Catalytic Mechanism of Lid Loop-Mediated Proton Transfer Revealed in the Fe/alpha-KG-Dependent Decarboxylase TraH
Authors: Zheng, X. / Zheng, L. / Bange, G.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epimerase opaE
B: Epimerase opaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4575
Polymers59,1682
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-54 kcal/mol
Surface area21110 Å2
Unit cell
Length a, b, c (Å)118.870, 118.870, 213.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Epimerase opaE / Oxepinamide F biosynthesis cluster protein E


Mass: 29584.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus ustus (mold) / Gene: opaE, HK57_00061 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0C1EFK1, Isomerases; Racemases and epimerases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 15-20% (v/v) PEG 300, 7.5-10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.65→39.72 Å / Num. obs: 116487 / % possible obs: 99.75 % / Redundancy: 10.7 % / Biso Wilson estimate: 68.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.45
Reflection shellResolution: 2.65→2.76 Å / Num. unique obs: 12975 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
PHENIXdev.5306refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→39.72 Å / SU ML: 0.3695 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.242
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2511 2562 5 %
Rwork0.2302 48669 -
obs0.2312 51231 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.66 Å2
Refinement stepCycle: LAST / Resolution: 2.65→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 15 0 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933898
X-RAY DIFFRACTIONf_angle_d1.04615293
X-RAY DIFFRACTIONf_chiral_restr0.0574624
X-RAY DIFFRACTIONf_plane_restr0.0081688
X-RAY DIFFRACTIONf_dihedral_angle_d18.0611454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.70.28681430.30772713X-RAY DIFFRACTION100
2.7-2.760.38731390.30372647X-RAY DIFFRACTION100
2.76-2.820.331410.30622667X-RAY DIFFRACTION100
2.82-2.880.33461410.30752687X-RAY DIFFRACTION100
2.88-2.960.30221400.29272661X-RAY DIFFRACTION100
2.96-3.040.32311420.30532695X-RAY DIFFRACTION100
3.04-3.120.35961410.31572681X-RAY DIFFRACTION99.96
3.12-3.230.31791420.29692688X-RAY DIFFRACTION99.93
3.23-3.340.32461400.29342672X-RAY DIFFRACTION99.86
3.34-3.470.33281410.28872667X-RAY DIFFRACTION99.72
3.47-3.630.28721410.28682683X-RAY DIFFRACTION99.44
3.63-3.820.25861410.25242681X-RAY DIFFRACTION98.33
3.82-4.060.26581410.23212679X-RAY DIFFRACTION99.61
4.06-4.380.25071430.21042723X-RAY DIFFRACTION99.58
4.38-4.820.21281420.17652693X-RAY DIFFRACTION99.51
4.82-5.510.21291450.19222760X-RAY DIFFRACTION100
5.51-6.940.20791470.21562778X-RAY DIFFRACTION100
6.94-39.720.17991520.17152894X-RAY DIFFRACTION99.58

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