PDB-8abt: Crystal structure of NaLdpA in complex with the product analog Re...

ID or keywords:

Entry

Database: PDB / ID: 8abt

Title

Crystal structure of NaLdpA in complex with the product analog Resveratrol

Components

SnoaL-like domain-containing protein

Keywords

LYASE / lignin / dehydratase

Function / homology

SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / RESVERATROL / SnoaL-like domain-containing protein

Function and homology information

Biological species

Novosphingobium aromaticivorans DSM 12444 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.39 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	Jun 19, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8abt.cif.gz	326.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8abt.ent.gz	258 KB	Display	PDB format
PDBx/mmJSON format	8abt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8abt_validation.pdf.gz	482 KB	Display	wwPDB validaton report
Full document	8abt_full_validation.pdf.gz	486 KB	Display
Data in XML	8abt_validation.xml.gz	11.7 KB	Display
Data in CIF	8abt_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/8abt ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abt	HTTPS FTP

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Related structure data

Related structure data	8abuC 8abvC 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	#213 - Sep 2017 Sirtuins similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: SnoaL-like domain-containing protein

B: SnoaL-like domain-containing protein

hetero molecules

59.1 kDa, 2 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
89.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SnoaL-like domain-containing protein

hetero molecules

B: SnoaL-like domain-containing protein

hetero molecules

B: SnoaL-like domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.045, 78.045, 159.541
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	A-307- SO4
2	1	A-307- SO4
3	1	B-304- SO4
4	1	B-304- SO4
5	1	A-563- HOH
6	1	A-595- HOH
7	1	A-603- HOH
8	1	B-402- HOH
9	1	B-570- HOH
10	1	B-595- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 6 - 239 / Label seq-ID: 6 - 239

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	SnoaL-like domain-containing protein Mass: 28830.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria) Strain: ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199 Gene: Saro_2805 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G4I2
#2: Chemical	ChemComp-STL / RESVERATROL Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₂O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H₂O
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: 2.6 Å³/Da / Density % sol: 52.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2 M ammonium sulfate, 2% PEG 400, 0.1 M HEPES pH 7.5

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	45	1	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Diamond	I03	1	0.97625
SYNCHROTRON	Diamond	I23	2	2.7552

Detector

Type	ID	Detector	Date
DECTRIS EIGER2 XE 16M	1	PIXEL	Sep 23, 2020
DECTRIS PILATUS 12M	2	PIXEL	Sep 23, 2020

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97625	1
2	2.7552	1

Reflection

Entry-ID: 8ABT / % possible obs: 100 %

Resolution (Å)	Num. obs	Redundancy (%)	CC_1/2	R_merge(I) obs	R_pim(I) all	Diffraction-ID	Net I/σ(I)
1.39-51.57	110449	19.3	0.999	0.135	0.031	1	13.3
1.8-79.87	50920	46.3	1	0.091	0.013	2	33.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Diffraction-ID	% possible all
1.39-1.41	11.8	2.756	0.4	5506	0.35	0.826	1	99.7
1.8-1.84	15.2	0.788	4.5	2997	0.951	0.197	2	99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.39→51.568 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.238 / WR_factor R_work: 0.221 / SU B: 4.592 / SU ML: 0.085 / Average fsc free: 0.7679 / Average fsc work: 0.7811 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2588	5537	5.027 %
R_work	0.2372	104614	-
all	0.238	-	-
obs	-	110151	99.966 %

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: 18.765 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.099 Å²	-0.05 Å²	-0 Å²
2-	-	-0.099 Å²	0 Å²
3-	-	-	0.322 Å²

Refinement step

Cycle: LAST / Resolution: 1.39→51.568 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3797	0	84	413	4294

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	4005
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	3639
X-RAY DIFFRACTION	r_angle_refined_deg	1.826	1.644	5446
X-RAY DIFFRACTION	r_angle_other_deg	1.496	1.58	8359
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.155	5	475
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.099	21.79	229
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.656	15	630
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.574	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	470
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	4547
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	995
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	771
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	3347
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1883
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1788
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	323
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.114	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.199	0.2	73
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	222
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	53
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.037	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.222	1.537	1888
X-RAY DIFFRACTION	r_mcbond_other	1.221	1.536	1887
X-RAY DIFFRACTION	r_mcangle_it	1.875	2.3	2358
X-RAY DIFFRACTION	r_mcangle_other	1.875	2.302	2359
X-RAY DIFFRACTION	r_scbond_it	1.593	1.72	2117
X-RAY DIFFRACTION	r_scbond_other	1.523	1.7	2102
X-RAY DIFFRACTION	r_scangle_it	2.395	2.526	3085
X-RAY DIFFRACTION	r_scangle_other	2.344	2.494	3062
X-RAY DIFFRACTION	r_lrange_it	4.845	18.75	4650
X-RAY DIFFRACTION	r_lrange_other	4.623	18.11	4533
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.072	0.05	7533

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07162	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07162	0.05009

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
1.39-1.426	0.342	389	0.351	7743	0.35	8145	0.575	0.581	99.8404	0.354
1.426-1.465	0.32	382	0.343	7546	0.342	7928	0.395	0.379	100	0.346
1.465-1.508	0.348	400	0.325	7292	0.326	7693	0.486	0.505	99.987	0.329
1.508-1.554	0.344	370	0.311	7129	0.313	7503	0.647	0.69	99.9467	0.315
1.554-1.605	0.327	357	0.282	6864	0.284	7223	0.728	0.774	99.9723	0.278
1.605-1.661	0.311	368	0.278	6680	0.279	7052	0.779	0.786	99.9433	0.265
1.661-1.724	0.303	369	0.263	6380	0.265	6751	0.806	0.835	99.9704	0.246
1.724-1.794	0.264	320	0.244	6186	0.245	6510	0.869	0.872	99.9386	0.227
1.794-1.874	0.296	333	0.234	5935	0.237	6270	0.844	0.884	99.9681	0.213
1.874-1.965	0.266	302	0.23	5674	0.232	5976	0.882	0.892	100	0.213
1.965-2.071	0.284	291	0.232	5378	0.235	5670	0.882	0.894	99.9824	0.213
2.071-2.197	0.23	267	0.227	5143	0.227	5410	0.917	0.918	100	0.212
2.197-2.348	0.262	243	0.219	4813	0.221	5056	0.895	0.916	100	0.203
2.348-2.536	0.258	238	0.221	4471	0.223	4709	0.893	0.916	100	0.206
2.536-2.777	0.262	217	0.215	4137	0.217	4354	0.917	0.925	100	0.201
2.777-3.104	0.217	187	0.213	3732	0.213	3919	0.925	0.926	100	0.201
3.104-3.582	0.238	150	0.222	3314	0.222	3464	0.915	0.921	100	0.215
3.582-4.381	0.212	151	0.202	2792	0.203	2943	0.942	0.941	100	0.202
4.381-6.174	0.197	128	0.234	2154	0.231	2282	0.958	0.943	100	0.234
6.174-51.568	0.317	71	0.278	1220	0.28	1292	0.931	0.919	99.9226	0.281

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.1256	0.0398	-0.0494	0.0664	0.0159	0.0569	0.0118	0.0219	0.0075	0.003	-0.0071	0.0271	-0.0022	-0.0301	-0.0047	0.002	0.0008	-0.0069	0.0171	0.0022	0.072	24.5346	22.968	-18.63
2	0.1166	0.0428	-0.0332	0.1152	-0.0478	0.0347	0.0156	0.0042	0.0337	0.0294	-0.0055	-0.0128	-0.0208	0.0094	-0.0101	0.0137	-0.0054	-0.0026	0.0065	-0.0088	0.0711	7.039	12.5489	18.5082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	6 - 240
2	X-RAY DIFFRACTION	1	ALL	A	301
3	X-RAY DIFFRACTION	1	ALL	A	401
4	X-RAY DIFFRACTION	1	ALL	A	701
5	X-RAY DIFFRACTION	1	ALL	A	801
6	X-RAY DIFFRACTION	1	ALL	A	901
7	X-RAY DIFFRACTION	1	ALL	A	1101
8	X-RAY DIFFRACTION	2	ALL	B	6 - 241
9	X-RAY DIFFRACTION	2	ALL	B	301
10	X-RAY DIFFRACTION	2	ALL	B	401
11	X-RAY DIFFRACTION	2	ALL	B	501

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