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- PDB-9l4q: Crystal structure of the carbamoyl N-methyltransferase Asc-Orf2 c... -

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Basic information

Entry
Database: PDB / ID: 9l4q
TitleCrystal structure of the carbamoyl N-methyltransferase Asc-Orf2 complexed with SAH
ComponentsMethyltransferase small domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / N-methyltransferse / post-modification
Function / homology: / Methyltransferase small domain / Methyltransferase small domain / methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase small domain-containing protein
Function and homology information
Biological speciesAmycolatopsis alba DSM 44262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLi, Z.Y. / Zhu, D.Y. / Shen, Y.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: A Carbamoyl N -Methyltransferase Catalyzes N -Methylation of the Primary Amide in Ansacarbamitocin Biosynthesis.
Authors: Li, Z. / Yang, W. / Sun, Z. / Wang, H. / Lu, C. / Zhu, D. / Shen, Y.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase small domain-containing protein
B: Methyltransferase small domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3654
Polymers47,5962
Non-polymers7692
Water1,24369
1
A: Methyltransferase small domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1822
Polymers23,7981
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase small domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1822
Polymers23,7981
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.677, 45.761, 48.116
Angle α, β, γ (deg.)89.65, 89.83, 88.42
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Methyltransferase small domain-containing protein


Mass: 23797.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis alba DSM 44262 (bacteria)
Gene: CFP75_27000 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A229RJG8
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Tris-HCl, pH 7.0, 1.2 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.27→41.66 Å / Num. obs: 15338 / % possible obs: 93.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 31.23 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.107 / Net I/σ(I): 9
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1755 / CC1/2: 0.872 / Rrim(I) all: 0.478 / % possible all: 72.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→41.66 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.28 743 4.85 %
Rwork0.196 --
obs0.1996 15332 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 52 69 3459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083492
X-RAY DIFFRACTIONf_angle_d1.0274768
X-RAY DIFFRACTIONf_dihedral_angle_d7.675493
X-RAY DIFFRACTIONf_chiral_restr0.057511
X-RAY DIFFRACTIONf_plane_restr0.009627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.440.33271390.24832456X-RAY DIFFRACTION78
2.44-2.690.29191880.22492977X-RAY DIFFRACTION97
2.69-3.080.31521600.2063016X-RAY DIFFRACTION97
3.08-3.880.30021290.19353087X-RAY DIFFRACTION98
3.88-41.660.22511270.17363053X-RAY DIFFRACTION97

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