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- PDB-9k2f: Crystal Structure of CyaF/SAH in open conformational state -

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Basic information

Entry
Database: PDB / ID: 9k2f
TitleCrystal Structure of CyaF/SAH in open conformational state
ComponentsCyaF
KeywordsBIOSYNTHETIC PROTEIN / Cyanogramide / N-methyltransferase / Substrate promiscuity / Open conformation
Function / homologyMethyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / CyaF
Function and homology information
Biological speciesActinoalloteichus caeruleus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, R.J. / Zhang, L.P. / Zhu, Y.G. / Zhang, C.S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177119 China
National Natural Science Foundation of China (NSFC)22193072 China
CitationJournal: To Be Published
Title: The open conformation of CyaF, a N-methyltransferase Involved in Cyanogramide Biosynthesis
Authors: Chen, R.J. / Zhang, L.P. / Zhu, Y.G. / Zhang, C.S.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CyaF
D: CyaF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1804
Polymers56,4122
Non-polymers7692
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-39 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.355, 103.045, 122.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein CyaF


Mass: 28205.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CyaF, a N-methyltransferase for cyanogramide biosynthesis, identified from A. cyanogriseus WH1-2216-6
Source: (gene. exp.) Actinoalloteichus caeruleus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6M3FWK4
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 30% w/v PEG 2000,0.12 M Ethylene Glycols, 0.1 M Bicine pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jan 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.7→20.02 Å / Num. obs: 14619 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 42.86 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 1887 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20.02 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.879 / SU B: 16.346 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27794 712 4.9 %RANDOM
Rwork0.22179 ---
obs0.22456 13863 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.924 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20 Å20 Å2
2---0.17 Å20 Å2
3----2.59 Å2
Refinement stepCycle: 1 / Resolution: 2.7→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 52 14 3501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173290
X-RAY DIFFRACTIONr_angle_refined_deg1.481.6484915
X-RAY DIFFRACTIONr_angle_other_deg1.2541.5727561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1745452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17720178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61615486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3281532
X-RAY DIFFRACTIONr_chiral_restr0.0650.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9734.4791826
X-RAY DIFFRACTIONr_mcbond_other2.9724.4791826
X-RAY DIFFRACTIONr_mcangle_it4.716.7032272
X-RAY DIFFRACTIONr_mcangle_other4.7096.7032273
X-RAY DIFFRACTIONr_scbond_it2.834.7921758
X-RAY DIFFRACTIONr_scbond_other2.834.7931758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6317.0652644
X-RAY DIFFRACTIONr_long_range_B_refined7.15252.3423847
X-RAY DIFFRACTIONr_long_range_B_other7.15252.3383848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 51 -
Rwork0.322 989 -
obs--100 %

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