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- PDB-9l4v: The crystal structure of BurB-SMM-SAM complex -

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Basic information

Entry
Database: PDB / ID: 9l4v
TitleThe crystal structure of BurB-SMM-SAM complex
ComponentsBurB
KeywordsTRANSFERASE / DMSP synthesis / S-methyltransferase / SET domain / global sulfur cycle
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
: / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET domain / SET domain superfamily / SET domain
Similarity search - Domain/homology
: / S-ADENOSYLMETHIONINE / Post-SET domain-containing protein
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, C.Y. / Cao, H.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)42276102 China
National Natural Science Foundation of China (NSFC)332330001 China
CitationJournal: To Be Published
Title: Mechanistic insights into the dimethylsulfoniopropionate synthesis enzyme BurB
Authors: Li, C.Y. / Cao, H.Y.
History
DepositionDec 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7033
Polymers20,1401
Non-polymers5632
Water1,63991
1
A: BurB
hetero molecules

A: BurB
hetero molecules

A: BurB
hetero molecules

A: BurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,81112
Polymers80,5604
Non-polymers2,2518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area8430 Å2
ΔGint-13 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.079, 67.159, 103.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein BurB


Mass: 20140.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: C7S16_5251 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAW9CLV1
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1LUD / S-METHYL-METHIONINE / (3-azanyl-4-oxidanyl-4-oxidanylidene-butyl)-dimethyl-sulfanium


Type: L-peptide linking / Mass: 164.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.4, 11% (w/v) PEG 8000

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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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9956 / % possible obs: 98.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 39.25 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.038 / Rrim(I) all: 0.136 / Net I/σ(I): 30
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 974 / CC1/2: 0.96 / Rpim(I) all: 0.129 / Rrim(I) all: 0.467 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.98 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 495 4.97 %
Rwork0.188 --
obs0.1897 9956 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 37 91 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091313
X-RAY DIFFRACTIONf_angle_d1.1221777
X-RAY DIFFRACTIONf_dihedral_angle_d8.484181
X-RAY DIFFRACTIONf_chiral_restr0.079197
X-RAY DIFFRACTIONf_plane_restr0.009229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.25441230.20962267X-RAY DIFFRACTION96
2.53-2.890.28211240.20862364X-RAY DIFFRACTION99
2.89-3.640.24351200.20242366X-RAY DIFFRACTION99
3.64-45.980.1871280.17062464X-RAY DIFFRACTION98

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