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- PDB-8abv: Crystal structure of SpLdpA in complex with erythro-DGPD -

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Basic information

Entry
Database: PDB / ID: 8abv
TitleCrystal structure of SpLdpA in complex with erythro-DGPD
ComponentsSnoaL-like domain-containing protein
KeywordsLYASE / lignin / dehydratase
Function / homology: / SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Chem-LJL / Chem-LJU / SnoaL-like domain-containing protein
Function and homology information
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 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

Downloads & links

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Assembly

Deposited unit
A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3716
Polymers30,4501
Non-polymers9215
Water4,197233
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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)94,11418
Polymers91,3513
Non-polymers2,76315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19460 Å2
ΔGint-154 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.281, 71.281, 86.922
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-303-

SO4

21A-303-

SO4

31A-624-

HOH

41A-629-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.) Sphingomonas paucimobilis (bacteria) / Strain: NBRC 103272 / SYK-6 / Gene: SLG_12650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2IQR8

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-LJU / (1S,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: Chemical ChemComp-LJL / (1R,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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris pH 8.5

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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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.683→86.922 Å / Num. obs: 23171 / % possible obs: 86.5 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.044 / Net I/σ(I): 13.3
Reflection shellResolution: 1.683→1.782 Å / Redundancy: 19 % / Rmerge(I) obs: 2.506 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1160 / CC1/2: 0.599 / Rpim(I) all: 0.587 / % possible all: 58.7

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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: 1.683→86.922 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.618 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1768 1147 4.95 %
Rwork0.148 22023 -
all0.149 --
obs-23170 78.441 %
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: 23.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.046 Å20.023 Å20 Å2
2--0.046 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.683→86.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 63 233 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132137
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161945
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.6492897
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5824469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5422.063126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18215343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.41515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02525
X-RAY DIFFRACTIONr_nbd_refined0.2120.2434
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21728
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2985
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2180
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.234
X-RAY DIFFRACTIONr_nbd_other0.2010.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.230
X-RAY DIFFRACTIONr_mcbond_it1.6792.033977
X-RAY DIFFRACTIONr_mcbond_other1.682.032976
X-RAY DIFFRACTIONr_mcangle_it2.5023.0371220
X-RAY DIFFRACTIONr_mcangle_other2.5013.0381221
X-RAY DIFFRACTIONr_scbond_it2.792.361159
X-RAY DIFFRACTIONr_scbond_other2.7892.361160
X-RAY DIFFRACTIONr_scangle_it4.3443.4211676
X-RAY DIFFRACTIONr_scangle_other4.3433.4211677
X-RAY DIFFRACTIONr_lrange_it6.15824.6562530
X-RAY DIFFRACTIONr_lrange_other5.92723.9512467
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 freeFsc work% reflection obs (%)WRfactor Rwork
1.683-1.7270.326100.2981550.321550.8350.8037.65660.292
1.727-1.7740.274480.2577590.25821170.8310.82338.120.254
1.774-1.8250.28540.26212280.26220180.8630.85963.52820.251
1.825-1.8820.218970.23216790.23219920.8890.89489.15660.218
1.882-1.9430.183900.23311570.22819310.9190.88764.57790.211
1.943-2.0110.201780.19217820.19218600.930.9271000.169
2.011-2.0870.255520.1839660.18717990.8970.93656.5870.152
2.087-2.1720.172760.15416610.15517370.9520.9561000.127
2.172-2.2690.204500.15910610.16116500.9490.95567.33330.128
2.269-2.380.205760.13215460.13516220.9480.9671000.107
2.38-2.5080.165540.12614520.12715060.9690.9731000.103
2.508-2.660.188760.13613650.1414410.9690.9731000.115
2.66-2.8440.177660.12213100.12513760.9710.9781000.105
2.844-3.0710.158540.11812100.1212640.9770.9821000.103
3.071-3.3640.176500.12411270.12611770.9620.9781000.111
3.364-3.7610.166580.139060.13310760.9680.97889.59110.125
3.761-4.3410.131690.1278780.1279470.9830.9821000.127
4.341-5.3130.161450.1197760.1228210.9830.9861000.124
5.313-7.50.167290.166210.166500.9760.9791000.165
7.5-86.9220.197150.1843840.1843990.9560.9651000.197
Refinement TLS params.Method: refined / Origin x: 25.1264 Å / Origin y: 11.3346 Å / Origin z: 17.4785 Å
111213212223313233
T0.0057 Å2-0.007 Å20.0051 Å2-0.0086 Å2-0.0058 Å2--0.0122 Å2
L0.1143 °20.0215 °2-0.0179 °2-0.1084 °20.0042 °2--0.1038 °2
S-0.0043 Å °0.0034 Å °-0.0214 Å °0.0083 Å °-0.0098 Å °0.0238 Å °0.0232 Å °-0.0287 Å °0.014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA-1 - 242
2X-RAY DIFFRACTION1ALLA301
3X-RAY DIFFRACTION1ALLA401
4X-RAY DIFFRACTION1ALLA501
5X-RAY DIFFRACTION1ALLA502

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