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- PDB-7cm9: DMSP lyase DddX -

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Basic information

Entry
Database: PDB / ID: 7cm9
TitleDMSP lyase DddX
ComponentsDMSP lyase
KeywordsLYASE / ATP-dependent DMSP lyase
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesPsychrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.249 Å
AuthorsLi, C.Y. / Zhang, Y.Z.
CitationJournal: Elife / Year: 2021
Title: A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA.
Authors: Li, C.Y. / Wang, X.J. / Chen, X.L. / Sheng, Q. / Zhang, S. / Wang, P. / Quareshy, M. / Rihtman, B. / Shao, X. / Gao, C. / Li, F. / Li, S. / Zhang, W. / Zhang, X.H. / Yang, G.P. / Todd, J.D. ...Authors: Li, C.Y. / Wang, X.J. / Chen, X.L. / Sheng, Q. / Zhang, S. / Wang, P. / Quareshy, M. / Rihtman, B. / Shao, X. / Gao, C. / Li, F. / Li, S. / Zhang, W. / Zhang, X.H. / Yang, G.P. / Todd, J.D. / Chen, Y. / Zhang, Y.Z.
History
DepositionJul 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DMSP lyase
B: DMSP lyase
C: DMSP lyase
D: DMSP lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,19612
Polymers326,7834
Non-polymers2,4138
Water20,2851126
1
A: DMSP lyase
B: DMSP lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,5986
Polymers163,3912
Non-polymers1,2064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-55 kcal/mol
Surface area54280 Å2
MethodPISA
2
C: DMSP lyase
D: DMSP lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,5986
Polymers163,3912
Non-polymers1,2064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-62 kcal/mol
Surface area54310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.565, 88.798, 273.263
Angle α, β, γ (deg.)90.000, 99.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DMSP lyase


Mass: 81695.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1126 / 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: 2.63 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate (pH 5.5) and 20% (wt/vol) polyethylene glycol (PEG) 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. obs: 156349 / % possible obs: 97.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.054 / Rrim(I) all: 0.099 / Χ2: 0.709 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.293.30.41577210.8160.2610.4910.44995.9
2.29-2.333.30.38276390.8390.2410.4530.44996
2.33-2.383.30.34576610.8550.2190.4090.46196.4
2.38-2.423.20.30277150.8840.1930.3590.46596
2.42-2.483.20.26977050.9060.1740.3220.49695.7
2.48-2.5330.23775760.9120.1590.2860.49595.6
2.53-2.63.10.21276800.9340.140.2550.50796.2
2.6-2.673.20.18577020.9490.1190.220.51996.4
2.67-2.753.30.16877610.9620.1060.1990.53696.6
2.75-2.833.30.14977260.9660.0940.1760.55496.7
2.83-2.943.20.12677500.9740.0810.150.59896.7
2.94-3.053.10.10777760.9790.070.1280.63496.8
3.05-3.1930.09377540.9820.0630.1130.74496.8
3.19-3.363.30.08478610.9860.0540.10.78897.8
3.36-3.573.30.07578960.9880.0480.0890.88798.5
3.57-3.853.30.06779960.990.0430.080.95598.9
3.85-4.233.10.06380490.990.0420.0761.03599.5
4.23-4.853.40.06180260.9920.0380.0721.14699.9
4.85-6.13.30.06281380.990.040.0741.015100
6.1-503.30.0682170.9920.0390.0721.2899.2

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.249→30.676 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 7559 5.02 %
Rwork0.1842 142883 -
obs0.1865 150442 93.55 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.979 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 105.28 Å2 / Biso mean: 42.37 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å20 Å2-1.8226 Å2
2---3.6405 Å2-0 Å2
3---3.6235 Å2
Refinement stepCycle: final / Resolution: 2.249→30.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21243 0 144 1126 22513
Biso mean--49.35 39.16 -
Num. residues----2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821771
X-RAY DIFFRACTIONf_angle_d1.129557
X-RAY DIFFRACTIONf_chiral_restr0.0723435
X-RAY DIFFRACTIONf_plane_restr0.0053779
X-RAY DIFFRACTIONf_dihedral_angle_d18.2598131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2494-2.2750.27832400.2219426083
2.275-2.30170.27182080.2217431287
2.3017-2.32980.27842200.2265443086
2.3298-2.35930.29042300.2248442987
2.3593-2.39030.30342540.2262445589
2.3903-2.4230.28352380.2187450789
2.423-2.45760.28112180.2219450289
2.4576-2.49430.28492690.2342451489
2.4943-2.53330.30382170.2263456990
2.5333-2.57480.26632430.2247462091
2.5748-2.61920.30252310.231463191
2.6192-2.66680.29622430.2175468793
2.6668-2.7180.26882550.2239476293
2.718-2.77350.29222560.213465893
2.7735-2.83370.26242290.218480795
2.8337-2.89960.26472620.2084477794
2.8996-2.9720.24312560.2067479294
2.972-3.05230.26292560.2062483295
3.0523-3.14210.25242640.2042485895
3.1421-3.24340.23662760.2114487896
3.2434-3.35920.24652680.1987488597
3.3592-3.49350.23382400.1903500198
3.4935-3.65220.22082140.1801509399
3.6522-3.84440.20152780.1701500898
3.8444-4.08480.20313070.1583499999
4.0848-4.39930.18022980.14425083100
4.3993-4.84050.18692780.13935077100
4.8405-5.53740.19362680.16155178100
5.5374-6.9630.24612770.18465147100
6.963-30.6760.1742660.1419513297

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