PDB-7fhv: Crystal structure of Multi-functional Polysaccharide lyase Smlt14...

ID or keywords:

Entry

Database: PDB / ID: 7fhv

Title

Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 6.5

Components

Polysaccharide lyase

Keywords

LYASE / Anionic Polysaccharide lyase

Function / homology

Function and homology information

glucuronan lyase / glucuronan lyase activity / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / hyaluronate lyase / hyaluronate lyase activity / polysaccharide catabolic process / cell outer membrane / periplasmic space
Similarity search - Function

Biological species

Stenotrophomonas maltophilia K279a (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Pandey, S. / Berger, B.W. / Acharya, R.

Funding support

India,

United States, 2items

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473.
Authors: Pandey, S. / Mahanta, P. / Berger, B.W. / Acharya, R.

History

Deposition	Jul 30, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7fhv.cif.gz	141.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7fhv_validation.pdf.gz	449.2 KB	Display	wwPDB validaton report
Full document	7fhv_full_validation.pdf.gz	450.3 KB	Display
Data in XML	7fhv_validation.xml.gz	25.2 KB	Display
Data in CIF	7fhv_validation.cif.gz	36.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fh/7fhv ftp://data.pdbj.org/pub/pdb/validation_reports/fh/7fhv	HTTPS FTP

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Related structure data

Related structure data	7fhuSC 7fhwC 7fhxC 7fhyC 7fhzC 7fi0C 7fi1C 7fi2C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7fhx-1 7fhx-2 7fhw-1 7fhy-2 3atz-2 7fhz-d 4mhb-2 1hju-2 1icq-2 7fi0-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Polysaccharide lyase

B: Polysaccharide lyase

hetero molecules

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

1

A: Polysaccharide lyase

hetero molecules

defined by author&software
35.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Polysaccharide lyase

hetero molecules

defined by author&software
35.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.513, 58.213, 67.543
Angle α, β, γ (deg.)	71.326, 89.938, 74.862
Int Tables number	1
Space group name H-M	P1

#1: Protein	Polysaccharide lyase / PL / Alginate lyase / Endolytic polysaccharide lyase / Hyaluronate lyase / Multifunctional ...PL / Alginate lyase / Endolytic polysaccharide lyase / Hyaluronate lyase / Multifunctional polysaccharide lyase / Poly-beta-D-glucuronate lyase Mass: 35428.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria) Strain: K279a / Gene: Smlt1473 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: B2FHL8, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.25 Å³/Da / Density % sol: 45.32 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M LiSo4 monohydrate, 0.1M Sodium Cacodylate pH 6.5, 30% (w/v) PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54178 Å
Detector	Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Nov 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.28→53.02 Å / Num. obs: 26004 / % possible obs: 92.3 % / Redundancy: 2.52 % / CC_1/2: 0.992 / R_merge(I) obs: 0.082 / Net I/σ(I): 9.17
Reflection shell	Resolution: 2.28→2.38 Å / Redundancy: 1.05 % / R_merge(I) obs: 0.3383 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 3005 / CC_1/2: 0.753 / % possible all: 88.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7FHU

7fhu

Resolution: 2.28→53.006 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.884 / SU B: 7.501 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.524 / ESU R Free: 0.267
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2451	1304	5.02 %
R_work	0.1962	24673	-
all	0.199	-	-
obs	-	25977	92.209 %

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: 17.556 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.849 Å²	-0.663 Å²	0.152 Å²
2-	-	0.007 Å²	-0.203 Å²
3-	-	-	-1.113 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→53.006 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4809	0	37	299	5145

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	4973
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4517
X-RAY DIFFRACTION	r_angle_refined_deg	1.429	1.639	6771
X-RAY DIFFRACTION	r_angle_other_deg	1.294	1.587	10307
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.853	5	612
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.207	20.844	308
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.733	15	734
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.156	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	602
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5821
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1277
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1088
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	4206
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	2410
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2086
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	265
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.264	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.235	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.109	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.071	1.782	2454
X-RAY DIFFRACTION	r_mcbond_other	1.069	1.781	2453
X-RAY DIFFRACTION	r_mcangle_it	1.731	2.668	3064
X-RAY DIFFRACTION	r_mcangle_other	1.731	2.669	3065
X-RAY DIFFRACTION	r_scbond_it	1.268	1.926	2519
X-RAY DIFFRACTION	r_scbond_other	1.24	1.912	2496
X-RAY DIFFRACTION	r_scangle_it	2.049	2.841	3707
X-RAY DIFFRACTION	r_scangle_other	2.024	2.817	3672
X-RAY DIFFRACTION	r_lrange_it	3.394	20.681	5784
X-RAY DIFFRACTION	r_lrange_other	3.279	20.609	5733

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
2.28-2.339	0.316	105	0.268	1752	0.271	2117	0.841	0.834	87.7185	0.249
2.339-2.403	0.254	78	0.242	1666	0.243	1964	0.877	0.863	88.7984	0.221
2.403-2.473	0.295	79	0.213	1735	0.217	2013	0.88	0.898	90.1143	0.189
2.473-2.549	0.258	99	0.191	1621	0.195	1901	0.894	0.919	90.4787	0.166
2.549-2.632	0.287	84	0.199	1634	0.203	1881	0.888	0.914	91.3344	0.176
2.632-2.724	0.299	81	0.195	1574	0.2	1788	0.886	0.918	92.5615	0.174
2.724-2.827	0.226	91	0.187	1488	0.189	1715	0.915	0.93	92.07	0.168
2.827-2.942	0.263	90	0.179	1476	0.183	1685	0.913	0.937	92.9377	0.162
2.942-3.072	0.208	76	0.178	1418	0.18	1595	0.93	0.944	93.6677	0.167
3.072-3.221	0.209	67	0.184	1369	0.185	1533	0.944	0.95	93.6725	0.173
3.221-3.395	0.245	66	0.192	1311	0.195	1462	0.932	0.946	94.186	0.187
3.395-3.6	0.249	70	0.211	1189	0.214	1346	0.93	0.926	93.5364	0.202
3.6-3.847	0.257	60	0.213	1142	0.215	1301	0.903	0.929	92.3905	0.203
3.847-4.154	0.233	50	0.18	1093	0.183	1208	0.929	0.94	94.6192	0.174
4.154-4.547	0.238	49	0.178	1001	0.181	1114	0.939	0.947	94.2549	0.172
4.547-5.079	0.175	43	0.166	913	0.167	997	0.962	0.954	95.8877	0.162
5.079-5.856	0.191	47	0.2	803	0.199	891	0.956	0.952	95.3984	0.191
5.856-7.151	0.263	35	0.191	674	0.195	749	0.94	0.952	94.6595	0.186
7.151-10.022	0.191	21	0.161	528	0.162	579	0.966	0.965	94.8186	0.164
10.022-53.006	0.326	13	0.25	285	0.253	330	0.885	0.936	90.303	0.255

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