PDB-5ofz: PllA lectin, apo

ID or keywords:

Entry

Database: PDB / ID: 5ofz

Title

PllA lectin, apo

Components

Uncharacterized protein

Keywords

SUGAR BINDING PROTEIN / PllA / apo / lectin

Function / homology

Function and homology information

carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Photorhabdus luminescens subsp. laumondii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Photorhabdus luminescens lectin A (PllA): A new probe for detecting alpha-galactoside-terminating glycoconjugates.
Authors: Beshr, G. / Sikandar, A. / Jemiller, E.M. / Klymiuk, N. / Hauck, D. / Wagner, S. / Wolf, E. / Koehnke, J. / Titz, A.

History

Deposition	Jul 11, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ofz.cif.gz	202.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5ofz_validation.pdf.gz	441.6 KB	Display	wwPDB validaton report
Full document	5ofz_full_validation.pdf.gz	444.5 KB	Display
Data in XML	5ofz_validation.xml.gz	24.5 KB	Display
Data in CIF	5ofz_validation.cif.gz	36.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/of/5ofz ftp://data.pdbj.org/pub/pdb/validation_reports/of/5ofz	HTTPS FTP

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Related structure data

Related structure data	5oduC 5ofiC 5ofxC 1l7lS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ofx-6 5ofx-5 5ofx-3 5ofx-8 5ofx-9 5ofx-2 5ofx-1 5ofx-7 5ofx-4 4yk3-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

51.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

defined by author
Evidence: gel filtration, DLS
13 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein

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

3

C: Uncharacterized protein

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

4

D: Uncharacterized protein

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

Unit cell

Length a, b, c (Å)	92.107, 92.107, 164.182
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Uncharacterized protein Mass: 12969.544 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria) Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu2096 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N561
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uncharacterized protein

Mass: 12969.544 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu2096 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N561

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium citrate tribasic dihydrate pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97779 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97779 Å / Relative weight: 1
Reflection	Resolution: 1.75→46.054 Å / Num. obs: 81583 / % possible obs: 99.59 % / Redundancy: 6.1 % / R_merge(I) obs: 0.047 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.75→1.84 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.7 / Num. measured obs: 53807 / Num. unique all: 11537 / CC_1/2: 0.915 / R_pim(I) all: 0.186 / R_rim(I) all: 0.409 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1L7L

1l7l

Resolution: 1.75→46.054 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2131	4183	5.13 %
R_work	0.1939	-	-
obs	0.1948	81571	99.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→46.054 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3608	0	0	530	4138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3696
X-RAY DIFFRACTION	f_angle_d	0.999	5048
X-RAY DIFFRACTION	f_dihedral_angle_d	9.68	2180
X-RAY DIFFRACTION	f_chiral_restr	0.069	564
X-RAY DIFFRACTION	f_plane_restr	0.008	668

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 (%)
1.75-1.7699	0.3176	173	0.2896	2408	X-RAY DIFFRACTION	95
1.7699-1.7907	0.3173	160	0.2738	2438	X-RAY DIFFRACTION	96
1.7907-1.8126	0.2788	119	0.2551	2532	X-RAY DIFFRACTION	98
1.8126-1.8355	0.2796	109	0.2357	2545	X-RAY DIFFRACTION	99
1.8355-1.8597	0.2509	129	0.2193	2550	X-RAY DIFFRACTION	99
1.8597-1.8851	0.2338	153	0.197	2547	X-RAY DIFFRACTION	100
1.8851-1.9121	0.214	153	0.1914	2538	X-RAY DIFFRACTION	100
1.9121-1.9406	0.2151	117	0.1825	2577	X-RAY DIFFRACTION	100
1.9406-1.9709	0.2318	135	0.1874	2565	X-RAY DIFFRACTION	100
1.9709-2.0032	0.2273	140	0.1825	2601	X-RAY DIFFRACTION	100
2.0032-2.0378	0.2321	149	0.1815	2527	X-RAY DIFFRACTION	100
2.0378-2.0748	0.2121	131	0.1782	2564	X-RAY DIFFRACTION	100
2.0748-2.1147	0.2107	114	0.181	2609	X-RAY DIFFRACTION	100
2.1147-2.1579	0.1956	115	0.1775	2600	X-RAY DIFFRACTION	100
2.1579-2.2048	0.2086	140	0.1778	2535	X-RAY DIFFRACTION	100
2.2048-2.2561	0.1815	142	0.1753	2606	X-RAY DIFFRACTION	100
2.2561-2.3125	0.2112	150	0.1773	2568	X-RAY DIFFRACTION	100
2.3125-2.3751	0.2036	146	0.1901	2559	X-RAY DIFFRACTION	100
2.3751-2.4449	0.2104	148	0.1813	2575	X-RAY DIFFRACTION	100
2.4449-2.5239	0.2028	148	0.1805	2568	X-RAY DIFFRACTION	100
2.5239-2.614	0.2113	145	0.1846	2586	X-RAY DIFFRACTION	100
2.614-2.7187	0.2033	156	0.1841	2576	X-RAY DIFFRACTION	100
2.7187-2.8424	0.2157	148	0.184	2577	X-RAY DIFFRACTION	100
2.8424-2.9922	0.177	118	0.1884	2645	X-RAY DIFFRACTION	100
2.9922-3.1797	0.2012	141	0.1952	2608	X-RAY DIFFRACTION	100
3.1797-3.4251	0.2056	127	0.1803	2628	X-RAY DIFFRACTION	100
3.4251-3.7697	0.2112	139	0.1968	2626	X-RAY DIFFRACTION	100
3.7697-4.3148	0.1847	127	0.1832	2664	X-RAY DIFFRACTION	100
4.3148-5.4348	0.1973	152	0.1834	2674	X-RAY DIFFRACTION	100
5.4348-46.0694	0.2677	159	0.2582	2792	X-RAY DIFFRACTION	100

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	0.0307	-0.0264	-0.0009	0.0443	-0.0348	0.0245	-0.0469	-0.2004	0.1353	-0.1212	-0.0272	0.1109	-0.0213	-0.2345	0	0.1554	0.0084	0.0142	0.249	0.0069	0.2227	156.7755	45.1424	192.3641
2	0.0057	0.0074	-0.0006	0.0124	-0.0094	0.0186	-0.0251	-0.0451	0.0988	0.1298	0.232	-0.1024	-0.1385	-0.0509	-0.0001	0.1451	-0.023	-0.0014	0.2339	0.0149	0.2174	156.5346	39.8161	176.0781
3	0.2562	-0.0088	-0.3041	0.7419	-0.6121	1.0779	0.0137	-0.3782	-0.0205	-0.0653	0.0075	0.0709	0.043	0.0792	0.0017	-0.0052	-0.0178	0.0345	0.4271	0.0358	0.139	165.6816	39.7313	199.6085
4	0.293	0.2158	-0.0843	0.2123	0.0708	0.278	-0.0225	-0.1576	-0.1169	-0.0459	-0.0219	0.0324	-0.0428	0.0052	-0.0239	0.1047	-0.007	0.0087	0.2613	0.0353	0.1923	161.9431	34.6054	192.0603
5	0.7321	-0.1503	0.322	0.0471	-0.1055	0.2275	0.1575	-0.604	-0.1218	0.0538	-0.0258	-0.067	0.0336	0.0282	0.0843	0.1537	0.0001	0.0257	0.4096	0.0282	0.2038	155.3125	36.7761	203.6208
6	0.0146	0.0051	0.0011	0.0136	0.025	0.0226	0.0392	-0.0329	0.1623	-0.0581	0.0503	-0.0396	0.023	-0.0834	0.0002	0.1344	-0.0004	-0.0113	0.2576	-0.0197	0.1826	165.0882	45.1877	186.9237
7	0.0233	0.0088	-0.0038	0.0326	-0.0223	0.0162	-0.1678	0.0495	0.0876	-0.152	0.0662	0.0896	0.0174	-0.1506	-0.0001	0.2396	-0.0561	0.0199	0.25	-0.0024	0.2229	161.1799	38.1904	164.9894
8	0.0389	-0.0461	-0.0478	0.0352	0.0438	0.0603	0.0133	0.0837	-0.0971	-0.052	-0.0405	-0.1028	-0.1071	0.2274	0.0007	0.1149	0.0302	0.003	0.2662	0.0302	0.2112	187.3152	34.6458	189.6589
9	0.0777	0.0391	-0.1718	0.2252	-0.3389	0.6947	-0.0521	0.0843	-0.1888	-0.0273	-0.0129	0.1865	0.1745	0.3117	-0.0162	0.1265	-0.0118	-0.0184	0.2585	0.0219	0.1827	187.3278	46.7718	177.5882
10	0.1837	-0.1	-0.1069	0.4816	0.0931	0.8265	0.0475	-0.229	-0.0475	-0.06	0.013	0.0445	-0.0049	-0.0292	0.1707	0.0532	-0.0232	-0.0117	0.3193	0.0559	0.1615	178.3595	35.8868	198.6003
11	0.4092	0.0116	0.2259	0.668	0.126	0.2988	-0.0223	-0.1534	0.0763	0.0182	0.0005	-0.0831	-0.0907	0.0196	0.2195	0.0889	0.0034	-0.0186	0.2667	0.021	0.1688	182.0093	43.9854	194.2315
12	0.0143	-0.0177	-0.0426	0.1454	0.1862	0.4061	0.1135	-0.4573	-0.1046	0.0158	-0.0248	0.0416	-0.1001	-0.2249	0.0297	0.1458	0.0058	-0.0176	0.3062	0.0618	0.2183	188.7683	36.9712	203.495
13	0.0127	0.0136	0.0059	0.0164	-0.0256	0.0189	0.0148	0.1156	-0.0987	-0.1055	0.0423	-0.072	0.1212	-0.0593	0.0006	0.1491	-0.0108	-0.0075	0.2041	0.0337	0.2013	178.8976	36.9098	184.8268
14	0.0078	0.007	-0.004	0.0116	0.0014	0.0193	-0.0676	-0.1058	-0.0483	0.0747	0.0139	-0.1366	0.0483	0.1436	-0.0004	0.1527	-0.0119	-0.0072	0.2553	0.0243	0.2182	182.5653	53.418	168.6281
15	0.1	0.042	0.0422	0.1167	0.132	0.2213	-0.0248	0.1819	-0.2971	-0.024	0.0388	-0.4707	-0.0898	0.3425	0.0079	0.2222	0.0223	-0.1012	0.1999	0.007	0.3517	156.3037	12.3582	168.427
16	-0.0005	0.0036	0.0024	0.0243	0.0145	0.0142	-0.021	-0.0707	-0.1575	0.0927	0.1134	0.0417	0.1592	0.2715	0.0001	0.1919	-0.0085	0.004	0.2649	-0.021	0.2582	150.8067	19.1209	153.8017
17	0.8094	-0.3264	0.0364	0.304	-0.2202	0.2683	0.1057	-0.0443	-0.1119	0.2578	-0.178	-0.118	0.034	0.1314	-0.1865	0.3341	-0.1003	-0.102	0.1397	0.0641	0.1903	148.8594	14.3353	178.5039
18	1.5425	0.1534	0.7548	0.4553	0.1073	0.3763	0.1436	0.1706	-0.1395	0.0987	-0.0428	-0.146	0.1796	0.1158	0.0902	0.1997	-0.0261	-0.0389	0.0962	0.0183	0.1576	149.0188	21.0325	171.2362
19	0.3495	-0.1062	-0.3685	0.0353	0.1163	0.3925	0.4341	-0.0345	-0.3007	0.1792	-0.1113	-0.1291	0.0526	0.2434	0.0992	0.3283	-0.0858	-0.1562	0.2241	0.09	0.2871	158.8308	19.8111	180.1955
20	0.1891	-0.0471	0.0185	0.0218	-0.0319	0.4551	0.1654	0.1049	-0.1977	0.0268	-0.0762	-0.1522	0.0227	-0.0337	-0.0117	0.2395	-0.021	-0.0527	0.1613	0.0266	0.2478	147.0518	10.5504	165.3572
21	0.012	-0.0099	0.0119	0.0092	0.0064	0.0252	-0.0057	0.1666	0.108	0.0099	0.0471	-0.2793	0.061	0.1817	0.0013	0.2357	-0.0044	0.0017	0.2441	0.0182	0.2073	142.9133	20.703	144.7156
22	0.0912	0.2532	-0.1884	1.4478	-1.0356	0.7337	-0.1883	0.1024	-0.5574	-0.5728	0.0666	-0.1678	0.543	0.033	0.1072	0.2731	0.0198	0.1213	0.279	-0.0498	0.2529	180.6433	35.7339	152.7863
23	0.0396	0.0125	-0.011	0.1115	-0.1548	0.2161	-0.1161	0.0753	0.1325	-0.2329	-0.0916	-0.2606	0.1308	0.2509	-0.0101	0.2391	-0.0114	0.0637	0.1534	-0.0038	0.2475	172.5936	29.7033	166.6104
24	0.3804	-0.0643	-0.108	0.2323	-0.0351	0.194	-0.1019	0.1315	-0.0483	-0.1455	0.1848	0.0765	-0.0055	-0.0597	0.0865	0.2801	-0.1251	0.0276	0.2299	-0.0014	0.1438	174.8885	45.275	146.8553
25	0.1886	0.1491	-0.0152	0.0873	-0.0756	0.1866	-0.2322	0.1721	-0.1336	-0.2663	0.1887	0.1537	0.2951	-0.0982	-0.0052	0.3283	-0.1007	0.0192	0.2345	-0.0152	0.1957	169.4218	38.5982	151.6575
26	0.3861	-0.3793	0.0255	0.3733	-0.0285	0.0038	-0.0406	0.3312	-0.2962	-0.2479	-0.1638	0.1771	0.2438	-0.2514	-0.036	0.5341	-0.2196	0.15	0.4624	-0.2419	0.0433	175.1228	36.0591	139.8027
27	0.0076	0.0107	-0.0142	0.0289	0.0065	0.0244	-0.0588	-0.1218	-0.0545	-0.0392	0.0839	-0.1586	0.1381	0.0958	-0	0.1945	-0.0287	0.0521	0.1847	0.0018	0.1987	177.624	41.9245	159.9379
28	0.0832	-0.0212	-0.0375	0.0212	0.003	0.0507	0.0114	0.2226	-0.0362	-0.1965	-0.0366	-0.1834	0.1734	0.088	0.0005	0.1624	0.0078	0.0157	0.2273	0.0469	0.258	167.4788	30.4739	177.627

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 43 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 44 through 94 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 106 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 107 through 116 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 117 through 122 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 19 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 20 through 26 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 27 through 43 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 44 through 94 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 95 through 106 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 107 through 116 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 117 through 122 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3 through 19 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 20 through 26 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 27 through 43 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 44 through 94 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 95 through 106 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 107 through 116 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 117 through 122 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3 through 19 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 20 through 26 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 27 through 43 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 44 through 94 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 95 through 106 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 107 through 116 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 117 through 122 )

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