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- PDB-9lfq: Complex crystal structure of transaldolase AprG with GlcNAc from ... -

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Basic information

Entry
Database: PDB / ID: 9lfq
TitleComplex crystal structure of transaldolase AprG with GlcNAc from Streptoalloteichus tenebrarius
Components(AprG) x 3
KeywordsTRANSFERASE / transaldolase / Schiff-base intermediate
Function / homology: / : / : / DI(HYDROXYETHYL)ETHER
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

Downloads & links

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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)227,33222
Polymers225,3356
Non-polymers1,99716
Water8,341463
1
A: AprG
E: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7648
Polymers74,9902
Non-polymers7756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AprG
D: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7267
Polymers75,0722
Non-polymers6555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AprG
F: AprG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8417
Polymers75,2742
Non-polymers5685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.888, 140.715, 130.775
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ADEBCF

#1: Protein AprG


Mass: 37494.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (bacteria)
Gene: aprG / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein AprG


Mass: 37576.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (bacteria)
Gene: aprG / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein AprG


Mass: 37696.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (bacteria)
Gene: aprG / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 3 types, 8 molecules

#5: Sugar
ChemComp-A1EJ2 / D-Erythrose


Type: D-saccharide / Mass: 120.104 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-A1EJ0 / N-Acetylglucosamine


Type: D-saccharide / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 471 molecules

#4: Chemical ChemComp-A1EJ3 / ~{N}-(2-oxidanylideneethyl)ethanamide / N-(2-Oxoethyl)acetamide


Mass: 101.104 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 41.85 %
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: Jan 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.13→47.42 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(1.21.1_5286: ???)refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→36.87 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 5257 5.04 %RANDOM
Rwork0.2281 ---
obs0.2298 104235 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15658 0 0 463 16121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.463
X-RAY DIFFRACTIONf_dihedral_angle_d14.8785701
X-RAY DIFFRACTIONf_chiral_restr0.0372348
X-RAY DIFFRACTIONf_plane_restr0.0042850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.150.35062070.30113249X-RAY DIFFRACTION100
2.15-2.180.35531610.29523320X-RAY DIFFRACTION100
2.18-2.210.3181490.30013382X-RAY DIFFRACTION100
2.21-2.230.3311950.29313206X-RAY DIFFRACTION100
2.23-2.260.30582000.2843253X-RAY DIFFRACTION100
2.26-2.290.30611710.28413374X-RAY DIFFRACTION100
2.29-2.330.31481860.27723224X-RAY DIFFRACTION100
2.33-2.360.31151510.27873296X-RAY DIFFRACTION100
2.36-2.40.31761550.27573389X-RAY DIFFRACTION100
2.4-2.440.31091710.27453239X-RAY DIFFRACTION100
2.44-2.480.30281670.28123277X-RAY DIFFRACTION100
2.48-2.530.35821470.27933367X-RAY DIFFRACTION100
2.53-2.570.3221390.27693265X-RAY DIFFRACTION100
2.57-2.630.2961750.26523343X-RAY DIFFRACTION100
2.63-2.680.28371920.27093265X-RAY DIFFRACTION100
2.68-2.750.34371740.25843289X-RAY DIFFRACTION100
2.75-2.810.28461720.25883266X-RAY DIFFRACTION100
2.81-2.890.28971850.25673304X-RAY DIFFRACTION99
2.89-2.980.29342080.26053253X-RAY DIFFRACTION100
2.98-3.070.29951750.25413309X-RAY DIFFRACTION100
3.07-3.180.30581680.24863259X-RAY DIFFRACTION100
3.18-3.310.28331900.24563328X-RAY DIFFRACTION100
3.31-3.460.31711850.23593241X-RAY DIFFRACTION99
3.46-3.640.23831970.20793264X-RAY DIFFRACTION100
3.64-3.870.21571760.20473340X-RAY DIFFRACTION100
3.87-4.170.27831810.18753292X-RAY DIFFRACTION100
4.17-4.590.18691560.17323351X-RAY DIFFRACTION100
4.59-5.250.19141830.18463338X-RAY DIFFRACTION100
5.25-6.60.21661930.20783338X-RAY DIFFRACTION100
6.61-36.870.19981480.18213357X-RAY DIFFRACTION99

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