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- PDB-9lfi: Crystal structure of transaldolase AprG from Streptoalloteichus t... -

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Basic information

Entry
Database: PDB / ID: 9lfi
TitleCrystal structure of transaldolase AprG from Streptoalloteichus tenebrarius
ComponentsAprG
KeywordsTRANSFERASE / transaldolase / Schiff-base intermediate
Function / homologySix-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / DI(HYDROXYETHYL)ETHER / AprG
Function and homology information
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsXie, Z.Z. / Li, Q.R. / Zhang, L.L. / Huang, J.-W. / He, Y.T. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: Apramycin Biosynthesis: Structure and Mechanism of Action of a New-Type Transaldolase AprG from Streptoalloteichus tenebrarius
Authors: Xie, Z. / Zhang, L. / Li, Q. / Huang, J.W. / He, Y. / Zhang, H. / Wang, X. / Min, J. / Chen, C.C. / Guo, R.T.
History
DepositionJan 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AprG
B: AprG
C: AprG
D: AprG
E: AprG
F: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,49911
Polymers224,9696
Non-polymers5315
Water15,367853
1
A: AprG
E: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0963
Polymers74,9902
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AprG
D: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0963
Polymers74,9902
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AprG
F: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3085
Polymers74,9902
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.784, 142.005, 129.821
Angle α, β, γ (deg.)90.00, 101.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AprG / Putative apramycin biosynthesis protein


Mass: 37494.781 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (bacteria)
Gene: aprG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6TDT8
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15 M Sodium acetate trihydrate; 29% polyethylene glycol 4,000; 0.1 M Tris ;pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.13→44.76 Å / Num. obs: 104303 / % possible obs: 99.8 % / Redundancy: 5.23 % / Rmerge(I) obs: 0.1188 / Net I/σ(I): 7.66
Reflection shellResolution: 2.13→2.16 Å / Rmerge(I) obs: 0.4483 / Num. unique obs: 4239

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→36.58 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 5263 5.16 %
Rwork0.2345 --
obs0.2367 102095 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15554 0 0 853 16407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.398
X-RAY DIFFRACTIONf_dihedral_angle_d3.9472258
X-RAY DIFFRACTIONf_chiral_restr0.0362325
X-RAY DIFFRACTIONf_plane_restr0.0042843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.150.39291540.29763069X-RAY DIFFRACTION94
2.15-2.180.34351650.29553112X-RAY DIFFRACTION95
2.18-2.210.32391530.28673209X-RAY DIFFRACTION95
2.21-2.230.33191560.28223096X-RAY DIFFRACTION95
2.23-2.260.34021730.27743170X-RAY DIFFRACTION96
2.26-2.290.32691700.27523215X-RAY DIFFRACTION96
2.29-2.330.32151630.28563103X-RAY DIFFRACTION96
2.33-2.360.37711760.28943132X-RAY DIFFRACTION95
2.36-2.40.32991950.28323254X-RAY DIFFRACTION98
2.4-2.440.34621790.27923197X-RAY DIFFRACTION99
2.44-2.480.36561910.28593230X-RAY DIFFRACTION99
2.48-2.530.341900.26943273X-RAY DIFFRACTION99
2.53-2.570.32731640.27353246X-RAY DIFFRACTION99
2.57-2.630.33031700.27913338X-RAY DIFFRACTION99
2.63-2.680.38091590.27883214X-RAY DIFFRACTION99
2.68-2.750.33741630.29663285X-RAY DIFFRACTION99
2.75-2.810.37941930.28093240X-RAY DIFFRACTION99
2.81-2.890.33861900.29013217X-RAY DIFFRACTION98
2.89-2.980.3332130.27063211X-RAY DIFFRACTION99
2.98-3.070.32061680.26983292X-RAY DIFFRACTION99
3.07-3.180.30151950.26713224X-RAY DIFFRACTION99
3.18-3.310.32091660.25653318X-RAY DIFFRACTION99
3.31-3.460.26951740.23133248X-RAY DIFFRACTION99
3.46-3.640.26961820.21883251X-RAY DIFFRACTION99
3.64-3.870.23861630.20043293X-RAY DIFFRACTION99
3.87-4.170.25132000.19173273X-RAY DIFFRACTION99
4.17-4.590.20232000.17543244X-RAY DIFFRACTION99
4.59-5.250.21591880.18573284X-RAY DIFFRACTION99
5.25-6.610.20341410.20333323X-RAY DIFFRACTION99
6.61-36.580.18241690.18433271X-RAY DIFFRACTION97

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