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- PDB-7wzg: Cypemycin N-terminal methyltransferase CypM -

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Basic information

Entry
Database: PDB / ID: 7wzg
TitleCypemycin N-terminal methyltransferase CypM
ComponentsCypemycin N-terminal methyltransferase
KeywordsTRANSFERASE / methyltransferase / cypemycin
Function / homologycypemycin N-terminal methyltransferase / peptide antibiotic biosynthetic process / N-methyltransferase activity / Methyltransferase domain 25 / Methyltransferase domain / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Cypemycin N-terminal methyltransferase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDuan, S.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural and mechanism analysis of cypm
Authors: Duan, S.Y.
History
DepositionFeb 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cypemycin N-terminal methyltransferase
B: Cypemycin N-terminal methyltransferase
C: Cypemycin N-terminal methyltransferase
D: Cypemycin N-terminal methyltransferase
E: Cypemycin N-terminal methyltransferase
F: Cypemycin N-terminal methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,64612
Polymers172,3406
Non-polymers2,3066
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-44 kcal/mol
Surface area55830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.111, 245.111, 81.653
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Cypemycin N-terminal methyltransferase


Mass: 28723.271 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: cypM / Production host: Escherichia coli (E. coli)
References: UniProt: E5KIC0, cypemycin N-terminal methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Final optimized conditions for YunM with SAM contained 1800 mM Ammonium sulfate, 100 mM CAPS/ Sodium hydroxide pH 10.4, 100 mM Lithium sulfate, and yielded square crystals.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 121720 / % possible obs: 90.38 % / Redundancy: 1.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.161 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 7270 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2→30.09 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 5672 5.1 %
Rwork0.1946 105590 -
obs0.1967 111262 90.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.83 Å2 / Biso mean: 28.4709 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 2→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10840 0 156 699 11695
Biso mean--20 33.68 -
Num. residues----1428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.316930.2252151224456
2.03-2.050.24541140.22832332244659
2.05-2.070.29181530.23912427258063
2.07-2.10.31661350.23682677281268
2.1-2.130.27911260.23822770289671
2.13-2.160.28991690.23442931310075
2.16-2.190.28941870.22673049323679
2.19-2.220.30821540.23643210336482
2.22-2.250.26511940.23563313350786
2.26-2.290.3071790.23263530370990
2.29-2.330.28781730.23213683385694
2.33-2.370.26712230.22773795401898
2.37-2.420.30481970.23863842403999
2.42-2.470.24072490.23043762401198
2.47-2.520.29152340.21573854408899
2.52-2.580.27541950.218138954090100
2.58-2.650.26282090.219438874096100
2.65-2.720.24892060.221538904096100
2.72-2.80.25432340.214738764110100
2.8-2.890.25912050.20939064111100
2.89-2.990.24252120.202438264038100
2.99-3.110.24042470.200438784125100
3.11-3.250.25122220.20033820404299
3.25-3.420.22241980.18339244122100
3.42-3.640.22141950.17738974092100
3.64-3.920.21461670.168339294096100
3.92-4.310.21991900.159739104100100
4.31-4.930.19411950.15393858405399
4.93-6.20.21052000.181339034103100
6.21-30.090.15882170.16113865408299

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