PDB-7fi2: Crystal structure of Multi-functional Polysaccharide lyase Smlt14...

ID or keywords:

Entry

Database: PDB / ID: 7fi2

Title

Crystal structure of Multi-functional Polysaccharide lyase Smlt1473-H168A from Stenotrophomonas maltophilia (strain K279a) at pH-5.0

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: 2.6 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 16, 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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Download

PDBx/mmCIF format	7fi2.cif.gz	79.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7fi2.ent.gz	55.1 KB	Display	PDB format
PDBx/mmJSON format	7fi2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7fi2_validation.pdf.gz	445.3 KB	Display	wwPDB validaton report
Full document	7fi2_full_validation.pdf.gz	446.4 KB	Display
Data in XML	7fi2_validation.xml.gz	13.7 KB	Display
Data in CIF	7fi2_validation.cif.gz	18.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/7fi2 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fi2	HTTPS FTP

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Related structure data

Related structure data	7fhuSC 7fhvC 7fhwC 7fhxC 7fhyC 7fhzC 7fi0C 7fi1C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7fhz-d 7fhx-1 7fhw-1 7fhw-2 7ci8-1 1e5n-1 4mhb-6 4h8n-2 7fhx-2 7fhv-1 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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	75.564, 75.564, 112.360
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#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: 35361.633 Da / Num. of mol.: 1 / Mutation: H168A 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-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.62 Å³/Da / Density % sol: 53.03 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M LiSo4 Monohydrate, 0.1M Sodium acetate trihdyrate pH-5.0 25% (w/v) PEG 3350

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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: 1.5418 Å
Detector	Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Dec 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.6→65.44 Å / Num. obs: 11515 / % possible obs: 96.4 % / Redundancy: 10.07 % / CC_1/2: 0.996 / R_merge(I) obs: 0.114 / Net I/σ(I): 16.59
Reflection shell	Resolution: 2.6→2.7 Å / Redundancy: 4.25 % / R_merge(I) obs: 0.3313 / Num. unique obs: 1013 / CC_1/2: 0.909 / % possible all: 78.3

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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: 2.6→65.309 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.891 / SU B: 9.059 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R: 0.844 / ESU R Free: 0.297
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2316	515	4.497 %
R_work	0.1873	10936	-
all	0.189	-	-
obs	-	11451	96.389 %

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: 20.782 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.272 Å²	-0.136 Å²	-0 Å²
2-	-	-0.272 Å²	0 Å²
3-	-	-	0.881 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→65.309 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2402	0	31	80	2513

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	2495
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2277
X-RAY DIFFRACTION	r_angle_refined_deg	1.568	1.64	3391
X-RAY DIFFRACTION	r_angle_other_deg	1.319	1.585	5196
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.399	5	307
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.998	20.719	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.381	15	362
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.006	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	302
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2908
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	636
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	616
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	2162
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	1212
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1108
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	83
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.053	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.471	2.086	1231
X-RAY DIFFRACTION	r_mcbond_other	1.437	2.083	1230
X-RAY DIFFRACTION	r_mcangle_it	2.43	3.121	1537
X-RAY DIFFRACTION	r_mcangle_other	2.438	3.125	1538
X-RAY DIFFRACTION	r_scbond_it	1.653	2.316	1264
X-RAY DIFFRACTION	r_scbond_other	1.646	2.308	1257
X-RAY DIFFRACTION	r_scangle_it	2.735	3.381	1854
X-RAY DIFFRACTION	r_scangle_other	2.74	3.368	1843
X-RAY DIFFRACTION	r_lrange_it	4.441	24.328	2910
X-RAY DIFFRACTION	r_lrange_other	4.424	24.336	2904

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
2.6-2.667	0.279	26	0.275	630	0.275	852	0.886	0.896	76.9953	0.233
2.667-2.74	0.422	33	0.24	681	0.247	845	0.82	0.919	84.497	0.193
2.74-2.82	0.285	33	0.217	712	0.22	813	0.907	0.933	91.6359	0.18
2.82-2.906	0.24	43	0.212	744	0.214	802	0.927	0.932	98.1297	0.173
2.906-3.001	0.244	32	0.204	716	0.206	754	0.927	0.935	99.2042	0.165
3.001-3.107	0.238	30	0.202	711	0.203	745	0.927	0.937	99.4631	0.169
3.107-3.224	0.311	26	0.19	701	0.194	727	0.904	0.944	100	0.161
3.224-3.355	0.264	12	0.194	679	0.195	691	0.949	0.953	100	0.174
3.355-3.504	0.167	30	0.181	642	0.18	672	0.962	0.959	100	0.165
3.504-3.674	0.194	27	0.167	617	0.168	644	0.959	0.964	100	0.152
3.674-3.872	0.274	33	0.17	578	0.176	612	0.929	0.961	99.8366	0.156
3.872-4.106	0.17	20	0.159	567	0.16	587	0.949	0.964	100	0.147
4.106-4.388	0.29	15	0.154	538	0.157	554	0.936	0.967	99.8195	0.148
4.388-4.738	0.252	34	0.148	469	0.155	503	0.939	0.968	100	0.142
4.738-5.188	0.248	33	0.166	444	0.172	477	0.947	0.965	100	0.158
5.188-5.795	0.132	23	0.205	411	0.201	434	0.959	0.959	100	0.184
5.795-6.683	0.161	26	0.189	367	0.188	393	0.963	0.963	100	0.179
6.683-8.164	0.179	19	0.162	319	0.163	339	0.963	0.976	99.705	0.159
8.164-11.456	0.177	14	0.15	247	0.151	262	0.968	0.977	99.6183	0.157
11.456-65.309	0.354	6	0.374	162	0.373	172	0.837	0.9	97.6744	0.328

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