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

ID or keywords:

Entry

Database: PDB / ID: 8abv

Title

Crystal structure of SpLdpA in complex with erythro-DGPD

Components

SnoaL-like domain-containing protein

Keywords

LYASE / 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 species

Sphingomonas paucimobilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.683 Å

Authors

Zahn, M. / Kuatsjah, E. / Beckham, G.T. / McGeehan, J.E.

Funding support

1items

Citation

Journal: 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. / ...

History

Deposition	Jul 4, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8abv.cif.gz	111.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8abv.ent.gz	79.7 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/8abv ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abv	HTTPS FTP

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Related structure data

Related structure data	8abtC 8abuC 8abwC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: SnoaL-like domain-containing protein

hetero molecules

31.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
Evidence: SAXS
94.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-303- SO4
2	1	A-303- SO4
3	1	A-624- HOH
4	1	A-629- HOH

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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 interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.17 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.683→86.922 Å / Num. obs: 23171 / % possible obs: 86.5 % / Redundancy: 19.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.194 / R_pim(I) all: 0.044 / Net I/σ(I): 13.3
Reflection shell	Resolution: 1.683→1.782 Å / Redundancy: 19 % / R_merge(I) obs: 2.506 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1160 / CC_1/2: 0.599 / R_pim(I) all: 0.587 / % possible all: 58.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NaLdpA

Resolution: 1.683→86.922 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.1768	1147	4.95 %
R_work	0.148	22023	-
all	0.149	-	-
obs	-	23170	78.441 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.274 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.046 Å²	0.023 Å²	0 Å²
2-	-	0.046 Å²	-0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.683→86.922 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2005	0	63	233	2301

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	2137
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1945
X-RAY DIFFRACTION	r_angle_refined_deg	1.879	1.649	2897
X-RAY DIFFRACTION	r_angle_other_deg	1.489	1.582	4469
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.172	5	245
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.54	22.063	126
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.182	15	343
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.4	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	243
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	2413
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	525
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	434
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	1728
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	985
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	986
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	180
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.172	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	121
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.16	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	1.679	2.033	977
X-RAY DIFFRACTION	r_mcbond_other	1.68	2.032	976
X-RAY DIFFRACTION	r_mcangle_it	2.502	3.037	1220
X-RAY DIFFRACTION	r_mcangle_other	2.501	3.038	1221
X-RAY DIFFRACTION	r_scbond_it	2.79	2.36	1159
X-RAY DIFFRACTION	r_scbond_other	2.789	2.36	1160
X-RAY DIFFRACTION	r_scangle_it	4.344	3.421	1676
X-RAY DIFFRACTION	r_scangle_other	4.343	3.421	1677
X-RAY DIFFRACTION	r_lrange_it	6.158	24.656	2530
X-RAY DIFFRACTION	r_lrange_other	5.927	23.951	2467

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.683-1.727	0.326	10	0.298	155	0.3	2155	0.835	0.803	7.6566	0.292
1.727-1.774	0.274	48	0.257	759	0.258	2117	0.831	0.823	38.12	0.254
1.774-1.825	0.28	54	0.262	1228	0.262	2018	0.863	0.859	63.5282	0.251
1.825-1.882	0.218	97	0.232	1679	0.232	1992	0.889	0.894	89.1566	0.218
1.882-1.943	0.183	90	0.233	1157	0.228	1931	0.919	0.887	64.5779	0.211
1.943-2.011	0.201	78	0.192	1782	0.192	1860	0.93	0.927	100	0.169
2.011-2.087	0.255	52	0.183	966	0.187	1799	0.897	0.936	56.587	0.152
2.087-2.172	0.172	76	0.154	1661	0.155	1737	0.952	0.956	100	0.127
2.172-2.269	0.204	50	0.159	1061	0.161	1650	0.949	0.955	67.3333	0.128
2.269-2.38	0.205	76	0.132	1546	0.135	1622	0.948	0.967	100	0.107
2.38-2.508	0.165	54	0.126	1452	0.127	1506	0.969	0.973	100	0.103
2.508-2.66	0.188	76	0.136	1365	0.14	1441	0.969	0.973	100	0.115
2.66-2.844	0.177	66	0.122	1310	0.125	1376	0.971	0.978	100	0.105
2.844-3.071	0.158	54	0.118	1210	0.12	1264	0.977	0.982	100	0.103
3.071-3.364	0.176	50	0.124	1127	0.126	1177	0.962	0.978	100	0.111
3.364-3.761	0.166	58	0.13	906	0.133	1076	0.968	0.978	89.5911	0.125
3.761-4.341	0.131	69	0.127	878	0.127	947	0.983	0.982	100	0.127
4.341-5.313	0.161	45	0.119	776	0.122	821	0.983	0.986	100	0.124
5.313-7.5	0.167	29	0.16	621	0.16	650	0.976	0.979	100	0.165
7.5-86.922	0.197	15	0.184	384	0.184	399	0.956	0.965	100	0.197

Refinement TLS params.

Method: refined / Origin x: 25.1264 Å / Origin y: 11.3346 Å / Origin z: 17.4785 Å

	11	12	13	21	22	23	31	32	33
T	0.0057 Å²	-0.007 Å²	0.0051 Å²	-	0.0086 Å²	-0.0058 Å²	-	-	0.0122 Å²
L	0.1143 °²	0.0215 °²	-0.0179 °²	-	0.1084 °²	0.0042 °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

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	-1 - 242
2	X-RAY DIFFRACTION	1	ALL	A	301
3	X-RAY DIFFRACTION	1	ALL	A	401
4	X-RAY DIFFRACTION	1	ALL	A	501
5	X-RAY DIFFRACTION	1	ALL	A	502

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