PDB-9ib6: Apo form of Tumor necrosis factor-like lectin PLTL from Photorhab...

ID or keywords:

Entry

Database: PDB / ID: 9ib6

Title

Apo form of Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii

Components

Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17

Keywords

SUGAR BINDING PROTEIN / lectin / TNF-like / Photorhabdus laumondii / PLTL / fucose-binding

Function / homology

: / Bc2l-C, N-terminal domain / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17

Function and homology information

Biological species

Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.2 Å

Authors

Melicher, F. / Wimmerova, M.

Funding support

Czech Republic, 1items

Citation

Journal: Febs J. / Year: 2025
Title: Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.
Authors: Melicher, F. / Dobes, P. / Komarek, J. / Faltinek, L. / Korsak, M. / Sykorova, P. / Houser, J. / Wimmerova, M.

History

Deposition	Feb 11, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	9ib6_validation.pdf.gz	417.4 KB	Display	wwPDB validaton report
Full document	9ib6_full_validation.pdf.gz	417.4 KB	Display
Data in XML	9ib6_validation.xml.gz	9.2 KB	Display
Data in CIF	9ib6_validation.cif.gz	12.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/9ib6 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/9ib6	HTTPS FTP

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Related structure data

Related structure data	9ib7C 9ib8C 9ib9C 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

Deposited unit

A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17

hetero molecules

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

1

A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17

hetero molecules

x 6

defined by author&software
Evidence: equilibrium centrifugation
89.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_555	y,x,-z	1
crystal symmetry operation	5_555	x-y,-y,-z	1
crystal symmetry operation	6_555	-x,-x+y,-z	1

Unit cell

Length a, b, c (Å)	83.501, 83.501, 105.577
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-302- HOH
2	1	A-337- HOH

#1: Protein	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17 Mass: 14951.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) Gene: plu4240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MZP1
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.37 Å³/Da / Density % sol: 48.07 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: sodium chloride, sodium citrate,

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.2→42.673 Å / Num. obs: 44331 / % possible obs: 100 % / Redundancy: 19.7 % / CC_1/2: 1 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.2→1.26 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6417 / CC_1/2: 0.842 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
SCALA		data scaling
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.2→42.673 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.971 / SU B: 1.588 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1815	2077	4.685 %
R_work	0.1571	42254	-
all	0.158	-	-
obs	-	44331	99.959 %

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: 14.847 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.279 Å²	-0.139 Å²	0 Å²
2-	-	-0.279 Å²	-0 Å²
3-	-	-	0.904 Å²

Refinement step

Cycle: LAST / Resolution: 1.2→42.673 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1004	0	1	97	1102

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	1098
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1015
X-RAY DIFFRACTION	r_angle_refined_deg	1.794	1.761	1518
X-RAY DIFFRACTION	r_angle_other_deg	0.635	1.709	2354
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.079	5	154
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.283	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.991	10	168
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.83	10	43
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	177
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1328
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	258
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	153
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	911
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	550
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.094	0.2	585
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.084	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.118	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.136	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.234	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	4.247	1.43	564
X-RAY DIFFRACTION	r_mcbond_other	4.09	1.428	563
X-RAY DIFFRACTION	r_mcangle_it	5.535	2.589	710
X-RAY DIFFRACTION	r_mcangle_other	5.553	2.59	711
X-RAY DIFFRACTION	r_scbond_it	6.181	1.665	534
X-RAY DIFFRACTION	r_scbond_other	6.176	1.665	535
X-RAY DIFFRACTION	r_scangle_it	8.525	2.961	798
X-RAY DIFFRACTION	r_scangle_other	8.519	2.961	799
X-RAY DIFFRACTION	r_lrange_it	12.209	14.927	1176
X-RAY DIFFRACTION	r_lrange_other	11.357	14.555	1157
X-RAY DIFFRACTION	r_rigid_bond_restr	4.07	3	2113

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
1.2-1.231	0.267	211	0.246	3041	0.248	3252	0.975	0.977	100	0.214
1.231-1.265	0.227	160	0.233	2995	0.233	3155	0.976	0.978	100	0.198
1.265-1.301	0.279	135	0.214	2965	0.216	3100	0.954	0.981	100	0.179
1.301-1.342	0.185	124	0.19	2839	0.19	2964	0.982	0.984	99.9663	0.157
1.342-1.385	0.219	138	0.17	2782	0.172	2921	0.981	0.987	99.9658	0.136
1.385-1.434	0.216	170	0.163	2619	0.166	2789	0.979	0.988	100	0.128
1.434-1.488	0.196	147	0.155	2593	0.157	2741	0.976	0.988	99.9635	0.124
1.488-1.549	0.177	111	0.142	2491	0.143	2604	0.983	0.989	99.9232	0.112
1.549-1.618	0.157	95	0.129	2409	0.13	2506	0.98	0.991	99.9202	0.104
1.618-1.696	0.168	114	0.123	2293	0.126	2407	0.981	0.991	100	0.101
1.696-1.788	0.162	75	0.12	2211	0.121	2287	0.987	0.992	99.9563	0.099
1.788-1.896	0.159	98	0.117	2075	0.119	2174	0.985	0.992	99.954	0.1
1.896-2.027	0.142	93	0.117	1939	0.118	2035	0.988	0.992	99.8526	0.103
2.027-2.189	0.135	86	0.127	1823	0.127	1909	0.99	0.991	100	0.114
2.189-2.397	0.166	63	0.151	1695	0.152	1758	0.985	0.986	100	0.135
2.397-2.679	0.191	64	0.159	1536	0.16	1600	0.98	0.984	100	0.146
2.679-3.091	0.191	58	0.159	1359	0.16	1418	0.982	0.986	99.9295	0.154
3.091-3.781	0.156	49	0.163	1158	0.163	1211	0.985	0.985	99.6697	0.163
3.781-5.327	0.179	68	0.158	886	0.16	954	0.981	0.986	100	0.168
5.327-42.673	0.269	18	0.244	545	0.245	563	0.962	0.964	100	0.245

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