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- PDB-9l4t: The crystal structure of BurB-Met complex -

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Basic information

Entry
Database: PDB / ID: 9l4t
TitleThe crystal structure of BurB-Met 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
METHIONINE / Post-SET domain-containing protein
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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
B: BurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5784
Polymers40,2802
Non-polymers2982
Water2,090116
1
A: BurB
B: BurB
hetero molecules

A: BurB
B: BurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1578
Polymers80,5604
Non-polymers5974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8150 Å2
ΔGint-23 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.954, 67.416, 59.251
Angle α, β, γ (deg.)90.00, 117.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BurB


Mass: 20140.023 Da / Num. of mol.: 2
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-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 15% (w/v) polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / 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: 2.15→50 Å / Num. obs: 22851 / % possible obs: 99.3 % / Redundancy: 6.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.059 / Rrim(I) all: 0.145 / Net I/σ(I): 27
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2159 / CC1/2: 0.91 / Rpim(I) all: 0.174 / Rrim(I) all: 0.422 / % possible all: 96.9

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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: 2.16→34.77 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1140 4.99 %
Rwork0.202 --
obs0.2041 22839 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 18 116 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082522
X-RAY DIFFRACTIONf_angle_d1.0333406
X-RAY DIFFRACTIONf_dihedral_angle_d6.662352
X-RAY DIFFRACTIONf_chiral_restr0.054374
X-RAY DIFFRACTIONf_plane_restr0.009446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.260.31711360.27692585X-RAY DIFFRACTION95
2.26-2.380.31731240.272710X-RAY DIFFRACTION99
2.38-2.530.31011330.25952711X-RAY DIFFRACTION99
2.53-2.720.26151470.25772730X-RAY DIFFRACTION100
2.72-30.29511570.24252702X-RAY DIFFRACTION100
3-3.430.27791540.22442712X-RAY DIFFRACTION100
3.43-4.320.22311480.17412754X-RAY DIFFRACTION100
4.32-34.770.18941410.16122795X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -13.8161 Å / Origin y: -1.7027 Å / Origin z: -8.2155 Å
111213212223313233
T0.3279 Å20.0123 Å2-0.0164 Å2-0.3848 Å2-0.004 Å2--0.3177 Å2
L2.7896 °20.0877 °2-0.2511 °2-0.6961 °20.1904 °2--0.8352 °2
S-0.0102 Å °0.6634 Å °-0.0897 Å °-0.0446 Å °0.0518 Å °0.0958 Å °-0.0648 Å °-0.1603 Å °0.0017 Å °
Refinement TLS groupSelection details: all

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