PDB-8abu: Crystal structure of NaLdpA mutant H97Q in complex with erythro-DGPD

ID or keywords:

Entry

Database: PDB / ID: 8abu

Title

Crystal structure of NaLdpA mutant H97Q 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-LJU / SnoaL-like domain-containing protein

Function and homology information

Biological species

Novosphingobium aromaticivorans DSM 12444 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.661 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	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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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PDBx/mmCIF format	8abu.cif.gz	492.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8abu.ent.gz	394.4 KB	Display	PDB format
PDBx/mmJSON format	8abu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8abu_validation.pdf.gz	745.4 KB	Display	wwPDB validaton report
Full document	8abu_full_validation.pdf.gz	750.1 KB	Display
Data in XML	8abu_validation.xml.gz	33.5 KB	Display
Data in CIF	8abu_validation.cif.gz	50.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/8abu ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abu	HTTPS FTP

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Related structure data

Related structure data	8abtC 8abvC 8abwC 7xxxS S: Starting model for refinement 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

B: SnoaL-like domain-containing protein

C: SnoaL-like domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: SAXS

Unit cell

Length a, b, c (Å)	113.384, 66.002, 107.051
Angle α, β, γ (deg.)	90.000, 108.675, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	B
6	3	C

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	A	A	8 - 241	8 - 241
2	2	1	LYS	LYS	B	B	8 - 241	8 - 241
3	3	2	TRP	TRP	A	A	8 - 242	8 - 242
4	4	2	TRP	TRP	C	C	8 - 242	8 - 242
5	5	3	LYS	LYS	B	B	7 - 241	7 - 241
6	6	3	LYS	LYS	C	C	7 - 241	7 - 241

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	SnoaL-like domain-containing protein Mass: 28820.516 Da / Num. of mol.: 3 / Mutation: H97Q 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-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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.19 Å³/Da / Density % sol: 43.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 500 MME, 10% PEG 20000, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M Imidazole/MES buffer pH 6.5

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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: Oct 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.661→56.234 Å / Num. obs: 69923 / % possible obs: 94 % / Redundancy: 7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.036 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.661→1.804 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.144 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3497 / CC_1/2: 0.653 / R_pim(I) all: 0.467 / % possible all: 55.1

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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: 7XXX

7xxx

Resolution: 1.661→56.234 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.959 / SU B: 5.036 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2009	3285	4.698 %
R_work	0.167	66639	-
all	0.169	-	-
obs	-	69923	79.105 %

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: 30.674 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.197 Å²	0 Å²	0.14 Å²
2-	-	-0.037 Å²	-0 Å²
3-	-	-	-0.207 Å²

Refinement step

Cycle: LAST / Resolution: 1.661→56.234 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5709	0	23	647	6379

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	5901
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5437
X-RAY DIFFRACTION	r_angle_refined_deg	1.701	1.642	8009
X-RAY DIFFRACTION	r_angle_other_deg	1.461	1.586	12487
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.385	5	700
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.549	21.959	342
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.429	15	943
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.836	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	700
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	6802
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1474
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1193
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	5058
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	2830
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	2882
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	628
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.196	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.117	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.253	0.2	16
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.045	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.175	2.647	2816
X-RAY DIFFRACTION	r_mcbond_other	2.175	2.646	2815
X-RAY DIFFRACTION	r_mcangle_it	3.36	3.948	3510
X-RAY DIFFRACTION	r_mcangle_other	3.36	3.95	3511
X-RAY DIFFRACTION	r_scbond_it	2.509	2.902	3085
X-RAY DIFFRACTION	r_scbond_other	2.509	2.904	3086
X-RAY DIFFRACTION	r_scangle_it	3.918	4.258	4499
X-RAY DIFFRACTION	r_scangle_other	3.917	4.26	4500
X-RAY DIFFRACTION	r_lrange_it	6.265	31.622	7125
X-RAY DIFFRACTION	r_lrange_other	6.035	30.866	6913
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.067	0.05	7445
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.073	0.05	7287
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.07	0.05	7405

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	0.06718	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06718	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07307	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.07307	0.05009
3	5	B	X-RAY DIFFRACTION	Local ncs	0.07036	0.05009
3	6	C	X-RAY DIFFRACTION	Local ncs	0.07036	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.661-1.704	0.231	4	0.299	167	X-RAY DIFFRACTION	2.6279
1.704-1.751	0.291	37	0.257	918	X-RAY DIFFRACTION	15.0678
1.751-1.801	0.276	97	0.247	2090	X-RAY DIFFRACTION	35.6073
1.801-1.857	0.291	196	0.247	3900	X-RAY DIFFRACTION	68.2212
1.857-1.918	0.258	276	0.242	4829	X-RAY DIFFRACTION	87.7751
1.918-1.985	0.264	258	0.228	5237	X-RAY DIFFRACTION	97.3083
1.985-2.06	0.242	276	0.205	5138	X-RAY DIFFRACTION	99.7605
2.06-2.144	0.223	230	0.185	4985	X-RAY DIFFRACTION	100
2.144-2.239	0.222	236	0.169	4751	X-RAY DIFFRACTION	99.9799
2.239-2.349	0.196	221	0.162	4588	X-RAY DIFFRACTION	99.9792
2.349-2.476	0.191	212	0.153	4346	X-RAY DIFFRACTION	99.9781
2.476-2.626	0.192	216	0.15	4127	X-RAY DIFFRACTION	100
2.626-2.807	0.193	176	0.152	3865	X-RAY DIFFRACTION	100
2.807-3.031	0.192	185	0.158	3608	X-RAY DIFFRACTION	100
3.031-3.32	0.192	153	0.162	3347	X-RAY DIFFRACTION	100
3.32-3.712	0.203	139	0.156	3012	X-RAY DIFFRACTION	99.9049
3.712-4.285	0.151	136	0.14	2659	X-RAY DIFFRACTION	100
4.285-5.246	0.168	113	0.133	2280	X-RAY DIFFRACTION	99.9582
5.246-7.409	0.209	93	0.178	1770	X-RAY DIFFRACTION	100
7.409-56.234	0.24	32	0.201	1022	X-RAY DIFFRACTION	99.5279

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	0.6458	0.1124	0.0134	0.0427	-0.0076	0.0048	-0.0155	0.1074	0.066	0.0241	0.0101	-0.0058	-0.0119	0.006	0.0054	0.0351	-0.0048	-0.015	0.0319	0.0188	0.0267	31.9059	1.0767	24.8415
2	0.2348	-0.1655	0.0082	0.185	-0.0271	0.0072	0.0184	0.0472	0.0049	0.0059	-0.002	0.0544	-0.0042	-0.009	-0.0165	0.0191	0.0091	0.0074	0.0294	0.0255	0.0544	7.1499	-3.0182	24.3983
3	0.2773	-0.0631	0.0094	0.2587	-0.021	0.0056	0.0193	0.0378	-0.0942	-0.0273	-0.0096	0.0093	0.0098	0.0074	-0.0097	0.0252	0.0097	-0.0136	0.0189	-0.0219	0.0389	22.6769	-22.1993	25.0352

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	8 - 242
2	X-RAY DIFFRACTION	2	ALL	B	3 - 242
3	X-RAY DIFFRACTION	3	ALL	C	7 - 242

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