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- PDB-23lq: Crystal structure of AprI -

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Basic information

Entry
Database: PDB / ID: 23lq
TitleCrystal structure of AprI
ComponentsPutative oxidase > apramycin biosynthesisN-methyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Apramycin / N-Methyltransferase
Function / homology: / Methyltransferase domain / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Release factor glutamine methyltransferase
Function and homology information
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsYu, Y. / Zhang, Q. / Zhang, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82304356 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Phosphate-tagged substrate recognition by a PrmC-like methyltransferase in apramycin biosynthesis.
Authors: Zhang, Q. / Zhang, Y. / Cui, Y. / Deng, Z. / Zhao, Q. / Long, F. / Yu, Y.
History
DepositionFeb 10, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Putative oxidase > apramycin biosynthesisN-methyltransferase
A: Putative oxidase > apramycin biosynthesisN-methyltransferase
C: Putative oxidase > apramycin biosynthesisN-methyltransferase
D: Putative oxidase > apramycin biosynthesisN-methyltransferase


Theoretical massNumber of molelcules
Total (without water)114,7544
Polymers114,7544
Non-polymers00
Water41423
1
A: Putative oxidase > apramycin biosynthesisN-methyltransferase

B: Putative oxidase > apramycin biosynthesisN-methyltransferase


Theoretical massNumber of molelcules
Total (without water)57,3772
Polymers57,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2880 Å2
ΔGint-27 kcal/mol
Surface area20760 Å2
MethodPISA
2
C: Putative oxidase > apramycin biosynthesisN-methyltransferase

D: Putative oxidase > apramycin biosynthesisN-methyltransferase


Theoretical massNumber of molelcules
Total (without water)57,3772
Polymers57,3772
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area2970 Å2
ΔGint-24 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.814, 135.661, 95.088
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative oxidase > apramycin biosynthesisN-methyltransferase / Release factor glutamine methyltransferase


Mass: 28688.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (bacteria)
Gene: aprI, LX15_005066 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2MFJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, Magnesium chloride, Sodium acetate, MOPS(3-Morpholinopropanesulfoinc Acid)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.51→45.22 Å / Num. obs: 35931 / % possible obs: 95 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.083 / Rrim(I) all: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 2.51→2.61 Å / Redundancy: 6.9 % / Rmerge(I) obs: 4.198 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3981 / CC1/2: 0.14 / Rpim(I) all: 2.559 / Rrim(I) all: 4.925 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX("2.1_6048": ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.19.2_4158phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→42.61 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 2001 5.62 %
Rwork0.216 --
obs0.2192 35592 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6844 0 0 23 6867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096963
X-RAY DIFFRACTIONf_angle_d1.0879447
X-RAY DIFFRACTIONf_dihedral_angle_d19.9642581
X-RAY DIFFRACTIONf_chiral_restr0.0541061
X-RAY DIFFRACTIONf_plane_restr0.0111264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.43831290.42922215X-RAY DIFFRACTION88
2.57-2.640.43251430.37632341X-RAY DIFFRACTION95
2.64-2.720.38341430.35712413X-RAY DIFFRACTION96
2.72-2.80.39611460.33132376X-RAY DIFFRACTION96
2.81-2.910.38291450.32022415X-RAY DIFFRACTION96
2.91-3.020.35321400.30032374X-RAY DIFFRACTION98
3.02-3.160.3431480.26122497X-RAY DIFFRACTION98
3.16-3.330.32621420.24852408X-RAY DIFFRACTION98
3.33-3.530.31181480.23072440X-RAY DIFFRACTION97
3.53-3.810.28331440.212394X-RAY DIFFRACTION97
3.81-4.190.24481440.19382471X-RAY DIFFRACTION99
4.19-4.790.24281500.17282486X-RAY DIFFRACTION98
4.8-6.040.24811400.1972365X-RAY DIFFRACTION95
6.04-42.610.20891390.17122396X-RAY DIFFRACTION94

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