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- PDB-23ks: Crystal structure of AprI/SAH complex -

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Basic information

Entry
Database: PDB / ID: 23ks
TitleCrystal structure of AprI/SAH complex
ComponentsRelease factor glutamine methyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Apramycin / N-Methyltransferase
Function / homology: / Methyltransferase domain / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Chem-SAO / Release factor glutamine methyltransferase
Function and homology information
Biological speciesStreptoalloteichus tenebrarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Release factor glutamine methyltransferase
C: Release factor glutamine methyltransferase
B: Release factor glutamine methyltransferase
D: Release factor glutamine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1858
Polymers112,6444
Non-polymers1,5424
Water4,792266
1
A: Release factor glutamine methyltransferase
hetero molecules

B: Release factor glutamine methyltransferase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, xml from PDBePISA: Analysis of protein interfaces suggests that the following quaternary structures are stable in solution. 1 2 A2a2 CD[DRG][2] 1 yes 20300.9 4658.15 - ...Evidence: gel filtration, xml from PDBePISA: Analysis of protein interfaces suggests that the following quaternary structures are stable in solution. 1 2 A2a2 CD[DRG][2] 1 yes 20300.9 4658.15 -24.7163 21.2326 2 A2a2 AB[DRG][2] 1 yes 20176.1 4398.52 -23.9937 19.2295 2 2 A2a2 CD[DRG][2] 1 yes 20300.9 4658.15 -24.7163 21.2326 1 Aa B[DRG] 2 yes 11696.8 754.799 0.78976 -0 1 Aa A[DRG] 2 yes 11370.4 752.557 1.16734 -0 3 2 A2a2 AB[DRG][2] 1 yes 20176.1 4398.52 -23.9937 19.2295 1 Aa C[DRG] 2 yes 11592.7 769.32 0.992532 -0 1 Aa D[DRG] 2 yes 11826.8 770.179 1.20654 -0
  • 57.1 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)57,0934
Polymers56,3222
Non-polymers7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area2860 Å2
ΔGint-27 kcal/mol
Surface area20170 Å2
MethodPISA
2
C: Release factor glutamine methyltransferase
hetero molecules

D: Release factor glutamine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0934
Polymers56,3222
Non-polymers7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3100 Å2
ΔGint-27 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.759, 75.255, 111.589
Angle α, β, γ (deg.)90.000, 105.894, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 28160.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus tenebrarius (strain ATCC 17920 / DSM 40477 / JCM 4838 / CBS 697.72 / NBRC 16177 / NCIMB 11028 / NRRL B-12390 / A12253. 1 / ISP 5477) (bacteria)
Gene: LX15_005066 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2MFJ8
#2: Chemical
ChemComp-SAO / 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 385.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H21N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
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: 2.3→36.31 Å / Num. obs: 45535 / % possible obs: 94.7 % / Redundancy: 9.4 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.051 / Rrim(I) all: 0.114 / Net I/σ(I): 16.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 4474 / CC1/2: 0.96 / Rpim(I) all: 0.221 / Rrim(I) all: 0.502 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Coot1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.87 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 1990 4.37 %
Rwork0.188 43514 -
obs0.19 45504 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 104 266 7414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747287
X-RAY DIFFRACTIONf_angle_d0.96029914
X-RAY DIFFRACTIONf_chiral_restr0.05011118
X-RAY DIFFRACTIONf_plane_restr0.01121318
X-RAY DIFFRACTIONf_dihedral_angle_d16.02952672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.25821400.21693103X-RAY DIFFRACTION97.1
2.36-2.420.27971370.21293121X-RAY DIFFRACTION97.6
2.42-2.490.26991380.20243015X-RAY DIFFRACTION95.6
2.49-2.570.2851380.21343055X-RAY DIFFRACTION96.32
2.57-2.660.28921450.22133111X-RAY DIFFRACTION98.52
2.66-2.770.2621490.2163139X-RAY DIFFRACTION98.15
2.77-2.90.30951400.21333126X-RAY DIFFRACTION98.4
2.9-3.050.26891480.20723134X-RAY DIFFRACTION99.03
3.05-3.240.28441370.20523065X-RAY DIFFRACTION95.7
3.24-3.490.21231390.18973054X-RAY DIFFRACTION96.23
3.49-3.840.2021460.17253184X-RAY DIFFRACTION99.05
3.84-4.40.22341470.16153166X-RAY DIFFRACTION98.75
4.4-5.530.18181430.16463067X-RAY DIFFRACTION95.25
5.54-32.870.19741430.17763174X-RAY DIFFRACTION96.48

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