PDB-7fi0: Crystal structure of Multi-functional Polysaccharide lyase Smlt14...

ID or keywords:

Entry

Database: PDB / ID: 7fi0

Title

Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in ManA bound form 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: 2.31 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	Nov 20, 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	7fi0.cif.gz	82.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7fi0_validation.pdf.gz	790.2 KB	Display	wwPDB validaton report
Full document	7fi0_full_validation.pdf.gz	792.2 KB	Display
Data in XML	7fi0_validation.xml.gz	15.3 KB	Display
Data in CIF	7fi0_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/7fi0 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fi0	HTTPS FTP

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Related structure data

Related structure data	7fhuSC 7fhvC 7fhwC 7fhxC 7fhyC 7fhzC 7fi1C 7fi2C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7fhw-2 7fhz-d 7fhw-1 7fhx-2 7fhy-2 3pb0-1 1v6y-d 7fhu-1 1nar-d 7fhv-2 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

36.2 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)	105.757, 160.662, 48.160
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-630- HOH

#1: Protein

Polysaccharide lyase / PL / Alginate lyase / Endolytic polysaccharide lyase / Hyaluronate lyase / Multifunctional ...

Mass: 35428.699 Da / Num. of mol.: 1
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: Polysaccharide

beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid

Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpAb1-4DManpAb1-4DManpAb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a1122A-1b_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-PEG / DI(HYDROXYETHYL)ETHER

Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

#4: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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: 2.89 Å³/Da / Density % sol: 57.4 % / Description: rod-shaped
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M LiSo4 Monohydrate, 0.1M Sodium acetate pH-5.0, 30% (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: 1.54178 Å
Detector	Type: BRUKER PHOTON 100 / Detector: CMOS / Date: May 13, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.31→29.45 Å / Num. obs: 17710 / % possible obs: 95.8 % / Redundancy: 6.39 % / CC_1/2: 0.989 / R_merge(I) obs: 0.155 / Net I/σ(I): 10.04
Reflection shell	Resolution: 2.31→2.41 Å / Redundancy: 2.88 % / R_merge(I) obs: 0.5597 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 1763 / CC_1/2: 0.578 / % possible all: 80.9

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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: 2.31→29.402 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.891 / Cross valid method: FREE R-VALUE / ESU R: 0.318 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2515	892	5.042 %
R_work	0.2049	16800	-
all	0.207	-	-
obs	-	17692	95.726 %

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: 20.624 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.726 Å²	0 Å²	0 Å²
2-	-	-1.397 Å²	0 Å²
3-	-	-	0.672 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→29.402 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2418	0	49	173	2640

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2535
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	2293
X-RAY DIFFRACTION	r_angle_refined_deg	1.604	1.663	3455
X-RAY DIFFRACTION	r_angle_other_deg	2.668	1.599	5246
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.45	5	307
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.332	20.833	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.484	15	370
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.311	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	317
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2938
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	642
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	642
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	2224
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1244
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1120
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.129	0.2	131
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.157	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.24	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.098	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.362	2.043	1231
X-RAY DIFFRACTION	r_mcbond_other	1.361	2.042	1230
X-RAY DIFFRACTION	r_mcangle_it	2.197	3.062	1537
X-RAY DIFFRACTION	r_mcangle_other	2.196	3.063	1538
X-RAY DIFFRACTION	r_scbond_it	1.792	2.279	1304
X-RAY DIFFRACTION	r_scbond_other	1.77	2.273	1300
X-RAY DIFFRACTION	r_scangle_it	2.951	3.335	1918
X-RAY DIFFRACTION	r_scangle_other	2.93	3.325	1913
X-RAY DIFFRACTION	r_lrange_it	4.294	24.36	3028
X-RAY DIFFRACTION	r_lrange_other	4.226	24.24	3001

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
2.31-2.37	0.372	55	0.303	987	0.306	1313	0.773	0.808	79.3602	0.262
2.37-2.434	0.288	63	0.273	1037	0.274	1316	0.86	0.843	83.5866	0.231
2.434-2.504	0.313	52	0.253	1071	0.256	1270	0.813	0.872	88.4252	0.211
2.504-2.581	0.264	50	0.24	1097	0.241	1219	0.907	0.893	94.0935	0.195
2.581-2.665	0.255	58	0.211	1157	0.213	1215	0.889	0.921	100	0.172
2.665-2.757	0.269	58	0.218	1115	0.221	1173	0.895	0.909	100	0.175
2.757-2.861	0.304	61	0.208	1035	0.214	1096	0.882	0.913	100	0.175
2.861-2.976	0.292	52	0.225	1034	0.228	1086	0.877	0.907	100	0.191
2.976-3.107	0.288	35	0.211	1003	0.214	1038	0.902	0.908	100	0.175
3.107-3.257	0.278	45	0.214	953	0.217	998	0.909	0.923	100	0.183
3.257-3.431	0.253	47	0.188	909	0.191	957	0.925	0.945	99.8955	0.164
3.431-3.636	0.22	61	0.196	823	0.198	889	0.953	0.948	99.4376	0.17
3.636-3.883	0.213	39	0.196	813	0.197	853	0.946	0.948	99.8828	0.17
3.883-4.188	0.257	42	0.178	757	0.182	799	0.926	0.956	100	0.155
4.188-4.578	0.189	54	0.158	695	0.16	749	0.958	0.964	100	0.139
4.578-5.103	0.187	30	0.162	644	0.163	676	0.968	0.968	99.7041	0.147
5.103-5.863	0.195	32	0.187	564	0.187	596	0.959	0.963	100	0.163
5.863-7.11	0.277	24	0.183	500	0.187	526	0.944	0.954	99.6198	0.166
7.11-9.774	0.213	23	0.162	404	0.165	427	0.964	0.969	100	0.148
9.774-29.402	0.251	11	0.232	203	0.233	271	0.948	0.956	78.9668	0.207

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