PDB-4gn5: OBody AM3L15 bound to hen egg-white lysozyme

ID or keywords:

Entry

Database: PDB / ID: 4gn5

Title

OBody AM3L15 bound to hen egg-white lysozyme

Components

Lysozyme C
OBody AM3L15

Keywords

DE NOVO PROTEIN/HYDROLASE / beta barrel / OB-fold / protein-protein complex / novel scaffold / muraminidase / enzyme inhibition / engineered binding protein / inhibitor / DE NOVO PROTEIN-HYDROLASE complex

Function / homology

Function and homology information

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...
Similarity search - Function

Biological species

Pyrobaculum aerophilum (archaea)

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.86 Å

Authors

Steemson, J.D. / Liddament, M.T.

Citation

Journal: Plos One / Year: 2014
Title: Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold.
Authors: Steemson, J.D. / Baake, M. / Rakonjac, J. / Arcus, V.L. / Liddament, M.T.

History

Deposition	Aug 16, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gn5.cif.gz	212.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4gn5.ent.gz	179.3 KB	Display	PDB format
PDBx/mmJSON format	4gn5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gn5_validation.pdf.gz	485.8 KB	Display	wwPDB validaton report
Full document	4gn5_full_validation.pdf.gz	494.2 KB	Display
Data in XML	4gn5_validation.xml.gz	29.3 KB	Display
Data in CIF	4gn5_validation.cif.gz	42.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gn/4gn5 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/4gn5	HTTPS FTP

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Related structure data

Related structure data	4glaC 4glvC 4gn3C 4gn4C C: citing same article (ref.)
Similar structure data	2rse-d 4gn4-d 5bvb-5 2vwv-d 1ouw-1 3va4-d 1sw1-1 2etm-1 2o68-d 3ppq-2 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	#21 - Sep 2001 Antibodies similarity (3) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #9 - Sep 2000 Lysozyme similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

A: OBody AM3L15

B: OBody AM3L15

C: Lysozyme C

D: Lysozyme C

hetero molecules

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

1

A: OBody AM3L15

D: Lysozyme C

hetero molecules

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

2

B: OBody AM3L15

C: Lysozyme C

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.990, 58.830, 95.180
Angle α, β, γ (deg.)	90.000, 95.430, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 4 molecules ABCD

#1: Protein	OBody AM3L15 Mass: 12379.253 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: aspS / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha]
#2: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 2 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme

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Non-polymers , 4 types, 610 molecules

#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 602 / 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	Density Matthews: 2.71 Å³/Da / Density % sol: 54.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M HEPES, 5% MPEG5000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å

Detector

Type: MAR 2300 / Detector: IMAGE PLATE / Date: Nov 17, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54179 Å / Relative weight: 1

Reflection

Redundancy: 2.8 % / Av σ(I) over netI: 7 / Number: 130001 / R_sym value: 0.082 / D res high: 1.86 Å / D res low: 94.753 Å / Num. obs: 46187 / % possible obs: 95.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
5.88	31.15	92.7	1	0.042	0.042	3.2
4.16	5.88	96.9	1	0.042	0.042	3.2
3.4	4.16	98.1	1	0.05	0.05	3.1
2.94	3.4	98.8	1	0.066	0.066	3
2.63	2.94	97.8	1	0.093	0.093	2.9
2.4	2.63	97.1	1	0.127	0.127	2.8
2.22	2.4	96.2	1	0.164	0.164	2.6
2.08	2.22	94.8	1	0.229	0.229	2.6
1.96	2.08	93.6	1	0.352	0.352	2.6
1.86	1.96	92.3	1	0.533	0.533	2.7

Reflection

Resolution: 1.86→94.753 Å / Num. all: 46187 / Num. obs: 46187 / % possible obs: 95.7 % / Redundancy: 2.8 % / R_sym value: 0.082 / Net I/σ(I): 8.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.86-1.96	2.7	0.533	1.4	17264	6490	0.533	92.3
1.96-2.08	2.6	0.352	2.2	16433	6203	0.352	93.6
2.08-2.22	2.6	0.229	3.1	15523	5892	0.229	94.8
2.22-2.4	2.6	0.164	4.3	14803	5603	0.164	96.2
2.4-2.63	2.8	0.127	5.8	14400	5197	0.127	97.1
2.63-2.94	2.9	0.093	7.3	13983	4754	0.093	97.8
2.94-3.4	3	0.066	9.8	12929	4252	0.066	98.8
3.4-4.16	3.1	0.05	11.3	11164	3574	0.05	98.1
4.16-5.88	3.2	0.042	13.5	8747	2745	0.042	96.9
5.88-31.15	3.2	0.042	12.4	4755	1477	0.042	92.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 38.92 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	31.15 Å
Translation	2.5 Å	31.15 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.16	data scaling
PHASER	2.1.4	phasing
PHENIX	1.6.1_357	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.86→31.15 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8755 / SU ML: 0.25 / σ(F): 0.01 / Phase error: 19.83 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2024	2189	5.05 %
R_work	0.1732	-	-
obs	0.1747	43335	89.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.252 Å² / k_sol: 0.344 e/Å³

Displacement parameters

B_iso max: 91.35 Å² / B_iso mean: 27.2552 Å² / B_iso min: 3.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.3713 Å²	0 Å²	-6.0967 Å²
2-	-	1.8311 Å²	0 Å²
3-	-	-	-3.2024 Å²

Refinement step

Cycle: LAST / Resolution: 1.86→31.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3665	0	73	602	4340

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.023	3979
X-RAY DIFFRACTION	f_angle_d	1.863	5419
X-RAY DIFFRACTION	f_chiral_restr	0.138	581
X-RAY DIFFRACTION	f_plane_restr	0.01	701
X-RAY DIFFRACTION	f_dihedral_angle_d	17.094	1437

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.86-1.9265	0.3008	184	0.2666	3552	3736	77
1.9265-2.0036	0.2948	179	0.2417	3685	3864	81
2.0036-2.0948	0.2894	212	0.2139	3865	4077	85
2.0948-2.2052	0.2417	205	0.1888	3980	4185	88
2.2052-2.3434	0.1974	239	0.1635	4091	4330	90
2.3434-2.5242	0.2034	255	0.1664	4225	4480	93
2.5242-2.7781	0.2166	215	0.1582	4341	4556	95
2.7781-3.1797	0.1775	230	0.1601	4426	4656	96
3.1797-4.0048	0.1601	250	0.144	4491	4741	97
4.0048-31.1543	0.1753	220	0.1543	4490	4710	95

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	1.1547	-0.3561	-0.3986	2.3208	2.2449	2.6465	0.4325	0.2813	-0.314	-0.3108	0.218	0.2809	0.1225	-0.0572	-0.2909	0.3203	-0.0587	-0.218	0.3127	0.0675	0.3104	10.6787	-3.3723	-10.4061
2	1.3769	-0.8503	1.533	1.6148	-0.9644	2.0206	0.1659	0.0633	-0.1387	-0.4442	0.1381	0.2793	0.1557	0.0417	-0.2237	0.1749	-0.0346	-0.058	0.1105	0.0299	0.1342	22.8678	-5.0576	-3.9883
3	0.9865	-0.6115	0.0435	0.8858	-0.3846	1.1698	0.0199	-0.0894	-0.0841	-0.2796	0.2826	0.4199	0.1707	-0.1913	-0.0807	0.1663	-0.057	-0.0655	0.1582	0.0693	0.1701	20.3941	-4.0338	1.2733
4	0.6798	-0.102	0.5966	0.23	0.1614	0.8036	0.306	0.2074	-0.5032	-0.514	0.2493	0.2889	0.5053	-0.1881	-0.4717	0.5883	0.0403	-0.2506	0.1959	-0.0098	0.3521	19.7938	-10.8489	-8.8114
5	1.3836	0.0336	-0.1235	0.4272	0.0798	0.334	-0.2371	0.2974	0.2935	-0.2871	-0.0295	-0.0392	-0.2569	0.473	0.2419	0.745	-0.0578	-0.0268	0.4686	0.0889	0.2633	24.8146	-0.1422	-18.8792
6	1.8544	-0.2492	0.1835	3.1584	-0.931	0.5523	0.0273	-0.4055	-0.3789	0.3658	0.6682	0.0919	0.3543	-0.1069	-0.376	0.6137	0.0295	-0.2429	0.3273	0.1441	0.2715	30.3606	-9.8125	66.0505
7	0.2806	0.4205	0.0434	0.7369	0.2413	0.4235	0.0273	-0.0425	0.0873	0.3544	0.0559	-0.1895	0.0346	0.1142	-0.0809	0.2142	0.0432	-0.0541	0.1389	-0.0475	0.1973	31.2199	-5.5936	53.399
8	1.1687	0.269	0.6412	1.0226	0.6814	0.9802	0.1049	-0.0465	-0.0512	0.3336	0.0029	-0.1076	0.1812	-0.0377	-0.1013	0.195	0.007	0.0043	0.0814	0.003	0.1082	21.2808	-8.8264	51.9115
9	1.0846	-0.1958	0.5683	1.7435	-0.0203	0.3539	-0.0074	0.0256	-0.0813	0.5673	0.0539	-0.1947	0.0853	0.1369	-0.075	0.3078	-0.012	-0.0374	0.0961	0.0019	0.1192	24.8489	-8.876	53.535
10	1.0236	0.0458	0.0001	0.3258	0.018	0.7515	-0.1664	0.1024	0.2319	-0.1041	0.0915	0.1804	-0.1487	-0.0797	0.0128	0.1116	-0.018	-0.0121	0.1155	0.0313	0.1469	8.9329	-7.5878	23.4999
11	0.4059	0.0071	-0.0678	0.7326	0.3833	0.5463	0.0144	-0.0268	-0.0712	0.0686	-0.0052	-0.1079	0.0393	-0.0207	-0.0221	0.1121	-0.0174	-0.0128	0.112	0.0118	0.1427	11.3604	-13.0782	32.3315
12	0.7686	0.3185	0.3805	1.4672	0.2798	1.2179	0.0437	-0.1914	0.0812	0.1612	-0.0894	0.1395	0.0398	-0.2993	0.0469	0.0576	-0.0033	0.0395	0.131	-0.0112	0.0789	5.8849	-8.7858	40.3922
13	0.557	-0.2851	-0.2333	0.3321	0.1302	0.2943	-0.0272	0.0394	-0.0805	0.1771	0.1143	-0.0727	-0.0776	0.0231	-0.0765	0.0415	0.0005	0.0444	0.1059	0.0197	0.0823	19.4735	-12.1303	23.0485
14	0.0129	-0.0282	0.1014	0.1175	-0.1724	0.6205	0.0408	0.0304	0.0508	0.0009	0.0147	-0.04	0.0671	0.3437	-0.0167	0.1252	0.0002	-0.0187	0.2369	-0.0277	0.1817	46.9418	-7.9981	20.3854
15	1.6877	0.1462	0.3853	0.0514	0.2048	2.9791	-0.0892	-0.125	0.5239	0.0894	-0.0329	-0.138	-0.7181	-0.0776	0.1837	0.1722	-0.0223	-0.0316	0.088	-0.0198	0.2111	39.2692	2.607	16.0336
16	2.0693	-0.4803	1.1587	1.5308	-0.1855	1.6612	0.0945	0.4169	-0.0451	-0.2184	-0.0195	-0.0764	0.0406	0.3756	-0.0354	0.1111	-0.0253	0.0244	0.198	-0.0217	0.1008	42.5626	-7.7507	4.369
17	1.8049	0.1282	0.2998	0.2568	-0.3272	0.5589	0.0999	-0.5682	-0.0829	0.0105	-0.0168	0.1014	0.1181	-0.4062	-0.1148	0.1403	-0.0553	-0.0007	0.2135	0.0275	0.1506	33.2061	-9.4102	21.0374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 1:8)	A	1 - 8
2	X-RAY DIFFRACTION	2	(chain A and resid 9:71)	A	9 - 71
3	X-RAY DIFFRACTION	3	(chain A and resid 72:96)	A	72 - 96
4	X-RAY DIFFRACTION	4	(chain A and resid 97:102)	A	97 - 102
5	X-RAY DIFFRACTION	5	(chain A and resid 103:108)	A	103 - 108
6	X-RAY DIFFRACTION	6	(chain B and resid 1:5)	B	1 - 5
7	X-RAY DIFFRACTION	7	(chain B and resid 6:31)	B	6 - 31
8	X-RAY DIFFRACTION	8	(chain B and resid 32:88)	B	32 - 88
9	X-RAY DIFFRACTION	9	(chain B and resid 89:107)	B	89 - 107
10	X-RAY DIFFRACTION	10	(chain C and resid 1:20)	C	1 - 20
11	X-RAY DIFFRACTION	11	(chain C and resid 21:47)	C	21 - 47
12	X-RAY DIFFRACTION	12	(chain C and resid 48:112)	C	48 - 112
13	X-RAY DIFFRACTION	13	(chain C and resid 113:129)	C	113 - 129
14	X-RAY DIFFRACTION	14	(chain D and resid 1:13)	D	1 - 13
15	X-RAY DIFFRACTION	15	(chain D and resid 14:24)	D	14 - 24
16	X-RAY DIFFRACTION	16	(chain D and resid 25:112)	D	25 - 112
17	X-RAY DIFFRACTION	17	(chain D and resid 113:127)	D	113 - 127

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