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- PDB-8abw: Crystal structure of SpLdpA in complex with threo-DGPD -

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Basic information

Entry
Database: PDB / ID: 8abw
TitleCrystal structure of SpLdpA in complex with threo-DGPD
ComponentsSnoaL-like domain-containing protein
KeywordsLYASE / lignin / dehydratase
Function / homology: / SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Chem-LHX / Chem-LJC / SnoaL-like domain-containing protein
Function and homology information
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsZahn, M. / Kuatsjah, E. / Beckham, G.T. / McGeehan, J.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation.
Authors: Kuatsjah, E. / Zahn, M. / Chen, X. / Kato, R. / Hinchen, D.J. / Konev, M.O. / Katahira, R. / Orr, C. / Wagner, A. / Zou, Y. / Haugen, S.J. / Ramirez, K.J. / Michener, J.K. / Pickford, A.R. / ...Authors: Kuatsjah, E. / Zahn, M. / Chen, X. / Kato, R. / Hinchen, D.J. / Konev, M.O. / Katahira, R. / Orr, C. / Wagner, A. / Zou, Y. / Haugen, S.J. / Ramirez, K.J. / Michener, J.K. / Pickford, A.R. / Kamimura, N. / Masai, E. / Houk, K.N. / McGeehan, J.E. / Beckham, G.T.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 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: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3796
Polymers30,4501
Non-polymers9295
Water2,558142
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,13818
Polymers91,3513
Non-polymers2,78715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area16780 Å2
ΔGint-150 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.983, 69.983, 85.892
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

21A-402-

SO4

31A-403-

SO4

41A-403-

SO4

51A-639-

HOH

61A-640-

HOH

71A-641-

HOH

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 30450.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Strain: NBRC 103272 / SYK-6 / Gene: SLG_12650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2IQR8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LJC / (1S,2S)-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol


Mass: 320.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LHX / (1R,2R)-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol


Mass: 320.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 0.2 M MgCl2, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.711→86.085 Å / Num. obs: 22162 / % possible obs: 94.7 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.038 / Net I/σ(I): 12.9
Reflection shellResolution: 1.711→1.85 Å / Redundancy: 19.8 % / Rmerge(I) obs: 2.398 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1107 / CC1/2: 0.623 / Rpim(I) all: 0.549 / % possible all: 55.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NaLdpA

Resolution: 1.83→85.892 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.129 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.207 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2289 706 4.356 %
Rwork0.176 15501 -
all0.178 --
obs-16207 73.682 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.227 Å20.113 Å20 Å2
2--0.227 Å2-0 Å2
3----0.735 Å2
Refinement stepCycle: LAST / Resolution: 1.83→85.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 61 142 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132112
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161909
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.6472865
X-RAY DIFFRACTIONr_angle_other_deg1.3551.5824385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.485241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66122.258124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1011514
X-RAY DIFFRACTIONr_chiral_restr0.080.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_nbd_refined0.220.2411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21788
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2138
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.234
X-RAY DIFFRACTIONr_nbd_other0.1790.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.223
X-RAY DIFFRACTIONr_mcbond_it1.3652.243967
X-RAY DIFFRACTIONr_mcbond_other1.3532.238966
X-RAY DIFFRACTIONr_mcangle_it2.213.351207
X-RAY DIFFRACTIONr_mcangle_other2.213.3551208
X-RAY DIFFRACTIONr_scbond_it2.1212.5481145
X-RAY DIFFRACTIONr_scbond_other2.122.5491146
X-RAY DIFFRACTIONr_scangle_it2.8053.7321658
X-RAY DIFFRACTIONr_scangle_other2.8043.7331659
X-RAY DIFFRACTIONr_lrange_it5.47826.442438
X-RAY DIFFRACTIONr_lrange_other5.44626.2192419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
1.83-1.8780.05410.32380.31516110.8512.42090.294
1.878-1.9290.1140.2391570.23315570.84610.34040.2310.959
1.929-1.9850.343140.2722600.27614980.7918.29110.2540.814
1.985-2.0460.305200.2935170.29314840.79736.1860.2740.77
2.046-2.1130.327450.2678360.27114190.80362.0860.2410.782
2.113-2.1870.275540.26212440.26314090.8292.12210.2410.837
2.187-2.270.294660.2512570.25213230.851000.2260.835
2.27-2.3620.282460.21812570.2213030.8771000.190.866
2.362-2.4670.252350.2111970.21112320.8981000.1860.854
2.467-2.5880.321370.19811500.20111870.9141000.1680.853
2.588-2.7280.277400.19210820.19511220.9271000.160.9
2.728-2.8930.274550.1810400.18410950.9411000.150.913
2.893-3.0920.205640.1689600.17110240.9461000.1430.94
3.092-3.340.28360.1579020.1619380.9541000.1410.923
3.34-3.6580.202490.1418300.1458790.9651000.1330.952
3.658-4.0890.18350.137650.1328000.9731000.1290.966
4.089-4.7190.165300.1236750.1257050.9791000.1240.973
4.719-5.7760.158290.1395920.146210.9741000.1380.981
5.776-8.150.179250.1684620.1684870.9631000.1680.966
8.15-85.8920.305210.1852800.1923010.9631000.20.928
Refinement TLS params.Method: refined / Origin x: -21.166 Å / Origin y: 17.1037 Å / Origin z: 16.9099 Å
111213212223313233
T0.0092 Å2-0.0148 Å20.0166 Å2-0.0585 Å2-0.0004 Å2--0.0602 Å2
L1.0622 °2-0.0061 °2-0.159 °2-1.3221 °2-0.0257 °2--0.4219 °2
S0.0002 Å °0.105 Å °-0.0069 Å °-0.065 Å °-0.0103 Å °-0.2512 Å °-0.0397 Å °0.1217 Å °0.0101 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA-1 - 240
2X-RAY DIFFRACTION1ALLA401
3X-RAY DIFFRACTION1ALLA501
4X-RAY DIFFRACTION1ALLA601
5X-RAY DIFFRACTION1ALLA603

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