PDB-4b5e: Crystal Structure of an amyloid-beta binding single chain antibod...

ID or keywords:

Entry

Database: PDB / ID: 4b5e

Title

Crystal Structure of an amyloid-beta binding single chain antibody PS2-8

Components

PS2-8

Keywords

IMMUNE SYSTEM / VHH / ALZHEIMER'S DISEASE

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

LAMA GLAMA (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.936 Å

Authors

Beringer, D.X. / Dorresteijn, B. / Rutten, L. / Wienk, H. / el Khattabi, M. / Kroon-Batenburg, L.M.J. / Verrips, C.T.

Citation

Journal: To be Published
Title: Amyloid-Beta Binding Single Chain Antibody Ps2-8
Authors: Beringer, D.X. / Dorresteijn, B. / Rutten, L. / Wienk, H. / El Khattabi, M. / Kroon-Batenburg, L.M.J. / Verrips, C.T.

History

Deposition	Aug 3, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 21, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 19, 2017	Group: Data collection
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow Item: _exptl_crystal_grow.temp
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4b5e.cif.gz	111 KB	Display	PDBx/mmCIF format
PDB format	pdb4b5e.ent.gz	87.5 KB	Display	PDB format
PDBx/mmJSON format	4b5e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4b5e_validation.pdf.gz	454.8 KB	Display	wwPDB validaton report
Full document	4b5e_full_validation.pdf.gz	456.3 KB	Display
Data in XML	4b5e_validation.xml.gz	13.1 KB	Display
Data in CIF	4b5e_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b5/4b5e ftp://data.pdbj.org/pub/pdb/validation_reports/b5/4b5e	HTTPS FTP

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Related structure data

Related structure data	4b41S S: Starting model for refinement
Similar structure data	3tyi-1 2cxb-2 5vk0-5 4k78-d 5vk0-1 1nmi-d 6d1r-d 2cxb-1 3sul-d 5ieo-d 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 - 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 (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: PS2-8

B: PS2-8

hetero molecules

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

1

A: PS2-8

hetero molecules

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

2

B: PS2-8

hetero molecules

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

Unit cell

Length a, b, c (Å)	24.647, 59.209, 133.635
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.9997, 0.0063, 0.0247), (0.0235, 0.6049, 0.796), (-0.0099, 0.7963, -0.6048)
Vector: 21.2622, -4.7605, -15.5783)

#1: Antibody	PS2-8 Mass: 13728.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMEK220 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H₂O
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: 1.78 Å³/Da / Density % sol: 31 % / Description: NONE
Crystal grow	Temperature: 291 K / pH: 6.5 Details: 0.2 M AMMONIUM SULFATE, 0.1 M NACITRATE PH 5.2, 26-28% PEGME5,000 TEMP 18 C

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Feb 28, 2011 / Details: MIRRORS
Radiation	Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.94→44.32 Å / Num. obs: 15145 / % possible obs: 98.8 % / Observed criterion σ(I): 3.5 / Redundancy: 6.9 % / B_iso Wilson estimate: 22.8 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shell	Resolution: 1.94→2.04 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B41

4b41

Resolution: 1.936→44.314 Å / SU ML: 0.23 / σ(F): 2.02 / Phase error: 22.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2356	1392	5 %
R_work	0.1812	-	-
obs	0.1841	27693	98.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 0 Å² / k_sol: 0 e/Å³

Displacement parameters

B_iso mean: 31.82 Å²

Refinement step

Cycle: LAST / Resolution: 1.936→44.314 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1910	0	27	106	2043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2001
X-RAY DIFFRACTION	f_angle_d	1.221	2701
X-RAY DIFFRACTION	f_dihedral_angle_d	11.84	721
X-RAY DIFFRACTION	f_chiral_restr	0.077	282
X-RAY DIFFRACTION	f_plane_restr	0.006	357

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 (%)
1.9365-2.0057	0.3136	127	0.2355	2416	X-RAY DIFFRACTION	90
2.0057-2.086	0.305	138	0.2222	2619	X-RAY DIFFRACTION	97
2.086-2.1809	0.2811	137	0.2093	2644	X-RAY DIFFRACTION	100
2.1809-2.2959	0.2451	140	0.2011	2636	X-RAY DIFFRACTION	98
2.2959-2.4397	0.2911	140	0.1982	2681	X-RAY DIFFRACTION	100
2.4397-2.6281	0.2846	138	0.203	2629	X-RAY DIFFRACTION	99
2.6281-2.8925	0.3139	143	0.1853	2676	X-RAY DIFFRACTION	100
2.8925-3.3109	0.2055	139	0.1725	2660	X-RAY DIFFRACTION	100
3.3109-4.171	0.1807	146	0.1498	2684	X-RAY DIFFRACTION	100
4.171-44.3256	0.1998	144	0.1679	2656	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	1.6681	-0.8637	0.3169	3.8432	1.6964	8.2546	0.2475	-0.3979	-0.547	0.428	0.2179	0.5357	0.7952	-1.3966	-0.3562	0.2054	-0.0483	0.0722	0.1981	0.0709	0.3705	1.3369	-5.4148	-17.6448
2	3.4287	-0.85	2.8247	6.0381	2.3386	2.0821	0.4358	0.4714	-0.3274	-0.5919	-0.1726	0.1731	0.7707	0.2472	-0.3666	0.2415	0.0791	-0.0335	0.2227	-0.1035	0.2455	5.942	-5.72	-30.4381
3	3.9674	0.2102	-2.8414	0.9367	0.3573	4.8822	0.1524	0.1771	0.4024	0.1123	-0.1235	0.1041	-0.1453	-0.3461	-0.0507	0.1415	0.0114	0.0062	0.1636	-0.0032	0.1911	1.8025	6.5456	-21.5503
4	3.3774	0.9976	-0.885	2.7211	1.4725	4.7367	0.1361	0.0136	0.1416	-0.0603	0.0438	-0.062	-0.2722	0.3565	-0.2512	0.1419	0.0067	0.014	0.202	0.0072	0.1815	14.1474	6.5635	-24.2301
5	2.6174	0.1743	-1.3342	3.7007	2.9781	5.4133	0.1012	-0.0379	-0.2633	-0.0154	0.1278	-0.2636	0.0722	0.3724	-0.0955	0.2109	0.0268	-0.0043	0.2584	0.0163	0.1926	12.2744	-5.5159	-26.505
6	2.6891	1.1085	-0.7005	5.4763	5.648	9.6455	-0.0465	0.1976	-0.2827	0.3081	0.2673	-0.2024	0.6658	0.8309	-0.0813	0.2045	0.0434	0.0077	0.1947	-0.0386	0.2628	8.8832	-5.7309	-24.8315
7	3.1115	0.6315	-0.7682	1.7098	0.4273	5.0763	0.2001	-0.2508	0.0006	0.3197	-0.0927	0.0689	0.1953	-0.1095	0.0258	0.2006	-0.0098	0.0249	0.1398	0.0084	0.2144	3.1119	2.3981	-15.6757
8	3.7381	0.8026	0.236	2.6353	-0.9542	9.0816	-0.128	0.2753	0.1273	-0.0208	0.0075	0.1331	0.0491	-0.0782	0.0647	0.1103	0.0362	0.0141	0.1006	-0.0285	0.2045	2.4852	5.9092	-26.4911
9	3.2579	-3.1434	2.7697	6.3398	-6.5554	7.5699	0.7804	0.265	-0.3842	-1.5131	-0.4183	0.1795	1.2346	0.935	-0.1184	0.4321	0.0621	-0.0671	0.3771	-0.0593	0.213	20.2739	-3.1727	0.9828
10	6.3996	-6.0818	5.2078	9.9751	-8.3355	2.1725	0.7459	0.2193	-0.8316	-1.1985	0.2633	0.9322	1.22	0.4229	-0.9902	0.5171	0.0845	-0.1773	0.3024	-0.0682	0.3256	15.9973	-6.7398	2.3387
11	5.8205	3.0152	-0.7516	8.4902	0.0658	2.8273	-0.0335	-0.0679	-0.3944	-0.0335	0.2227	0.4626	0.4262	-0.0515	-0.1956	0.1754	0.0071	-0.0469	0.1866	0.0043	0.1537	15.8695	-9.9134	13.5434
12	8.3235	8.6138	-6.7634	9.8698	-5.921	8.3547	0.765	-1.187	-0.1728	0.4963	-0.6362	-0.4662	-0.5917	0.8766	-0.2369	0.1912	0.0213	0.014	0.3216	-0.0253	0.3254	20.698	4.3557	12.7947
13	6.186	4.7149	-0.797	8.2219	-3.4523	5.0189	0.4853	-0.4814	-0.0853	0.3588	-0.1687	1.1624	-0.2447	-0.3914	-0.3749	0.1632	0.0121	0.0217	0.2627	0.031	0.3821	7.1609	-2.0347	14.2373
14	7.6113	4.5192	-0.9248	5.283	-4.4973	6.6172	-0.0413	0.6409	-1.179	-0.7917	0.3264	-0.0466	0.7951	-0.1405	-0.172	0.2921	0.0021	-0.0917	0.2749	-0.0312	0.4433	8.7784	-8.5518	7.0681
15	2.035	-8.869	-1.952	2.0313	-4.7172	5.0059	0.0237	0.0774	-1.4265	-2.2055	0.856	1.8446	1.0119	-0.6135	-0.756	0.4909	-0.0868	-0.1991	0.3826	0.0514	0.4583	12.2023	-8.0098	4.7662
16	5.8577	1.2237	1.8088	7.7745	-6.6818	9.7244	0.1308	0.19	0.4337	-0.0201	-0.2558	0.1459	-0.4014	0.3951	0.1363	0.1649	-0.0057	0.0399	0.1544	-0.0547	0.2069	17.6383	4.879	4.712
17	8.4498	4.0624	-0.3928	5.058	0.0102	3.7243	0.253	0.1144	-0.3287	0.6364	0.0573	-0.0246	-0.2564	-0.0627	-0.3387	0.2816	0.0179	-0.0266	0.3358	0.0527	0.1897	14.7909	-2.982	21.7142
18	5.0838	0.594	-0.2733	2.9242	-8.3776	9.5086	0.0625	0.2531	-0.2937	-0.0665	-0.2752	-0.3142	-0.0216	0.4546	0.1414	0.2842	0.023	-0.0509	0.1794	-0.0828	0.1993	22.9326	-1.6678	7.3614

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 2 THROUGH 17 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 18 THROUGH 32 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 33 THROUGH 52 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 53 THROUGH 67 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 68 THROUGH 76 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 77 THROUGH 83 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 84 THROUGH 99 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 100 THROUGH 127 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 1 THROUGH 17 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 18 THROUGH 25 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 26 THROUGH 39 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 40 THROUGH 52 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 53 THROUGH 67 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 68 THROUGH 76 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 77 THROUGH 83 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 84 THROUGH 99 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 100 THROUGH 113 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 114 THROUGH 127 )

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