PDB-5xcq: Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide

ID or keywords:

Entry

Database: PDB / ID: 5xcq

Title

Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide

Components

C8 peptide
VH-SARAH(Y35C)chimera
VL-SARAH(M24C) chimera

Keywords

IMMUNE SYSTEM /

antibody fragment / Fv-clasp

Function / homology

p53, subunit A / p53-like tetramerisation domain / Few Secondary Structures /

Irregular /

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.313 Å

Authors

Arimori, T. / Takagi, J.

Citation

Journal: Structure / Year: 2017
Title: Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability
Authors: Arimori, T. / Kitago, Y. / Umitsu, M. / Fujii, Y. / Asaki, R. / Tamura-Kawakami, K. / Takagi, J.

History

Deposition	Mar 23, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 2023	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	5xcq.cif.gz	162.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5xcq.ent.gz	126.1 KB	Display	PDB format
PDBx/mmJSON format	5xcq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xc/5xcq ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xcq	HTTPS FTP

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Related structure data

Related structure data	5xcrC 5xcsC 5xctC 5xcuC 5xcvC 5xcxC 2zpkS 4nr2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4xh0-d 2crk-d 3vw2-1 3e3q-6 1gng-1 2jlw-2 5gn1-2 4rm8-1 2xar-2 6cjw-d 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: VH-SARAH(Y35C)chimera

B: VL-SARAH(M24C) chimera

C: C8 peptide

hetero molecules

38.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	41.870, 89.230, 50.980
Angle α, β, γ (deg.)	90.00, 108.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	VH-SARAH(Y35C)chimera Mass: 19116.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli)
#2: Antibody	VL-SARAH(M24C) chimera Mass: 18148.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli)
#3: Protein/peptide	C8 peptide Mass: 873.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.37 Å³/Da / Density % sol: 48.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.1 M Bis-Tris (pH 5.5), 0.2 M Ammonium Sulfate, 20%(w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.31→48.48 Å / Num. obs: 84444 / % possible obs: 99.7 % / Redundancy: 7.5 % / R_sym value: 0.07 / Net I/σ(I): 16.91
Reflection shell	Resolution: 1.31→1.39 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.13 / R_sym value: 0.71 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2341: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZPK, 4NR2

2zpk

4nr2

Resolution: 1.313→39.818 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.23

	R_factor	Num. reflection	% reflection
R_free	0.1817	4242	5.02 %
R_work	0.1651	-	-
obs	0.1659	84437	99.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.313→39.818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2608	0	25	392	3025

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2900
X-RAY DIFFRACTION	f_angle_d	1.265	3982
X-RAY DIFFRACTION	f_dihedral_angle_d	18.743	1079
X-RAY DIFFRACTION	f_chiral_restr	0.1	434
X-RAY DIFFRACTION	f_plane_restr	0.009	522

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 (%)
1.3132-1.3281	0.2974	139	0.2516	2471	X-RAY DIFFRACTION	94
1.3281-1.3437	0.2446	129	0.2306	2717	X-RAY DIFFRACTION	100
1.3437-1.3601	0.2603	132	0.2213	2626	X-RAY DIFFRACTION	100
1.3601-1.3773	0.2421	148	0.2123	2687	X-RAY DIFFRACTION	100
1.3773-1.3955	0.2385	134	0.2035	2717	X-RAY DIFFRACTION	100
1.3955-1.4146	0.2063	143	0.205	2641	X-RAY DIFFRACTION	100
1.4146-1.4348	0.2208	143	0.1963	2666	X-RAY DIFFRACTION	100
1.4348-1.4562	0.2339	150	0.1953	2691	X-RAY DIFFRACTION	100
1.4562-1.479	0.2075	124	0.1947	2649	X-RAY DIFFRACTION	100
1.479-1.5032	0.2151	162	0.1864	2659	X-RAY DIFFRACTION	100
1.5032-1.5291	0.1762	134	0.182	2672	X-RAY DIFFRACTION	100
1.5291-1.5569	0.1977	140	0.1716	2712	X-RAY DIFFRACTION	100
1.5569-1.5869	0.169	139	0.1695	2656	X-RAY DIFFRACTION	100
1.5869-1.6193	0.1953	148	0.1628	2672	X-RAY DIFFRACTION	100
1.6193-1.6545	0.2186	155	0.1662	2667	X-RAY DIFFRACTION	100
1.6545-1.693	0.194	148	0.1607	2677	X-RAY DIFFRACTION	100
1.693-1.7353	0.1955	140	0.1605	2670	X-RAY DIFFRACTION	100
1.7353-1.7822	0.197	124	0.1612	2674	X-RAY DIFFRACTION	100
1.7822-1.8347	0.1916	152	0.1615	2701	X-RAY DIFFRACTION	100
1.8347-1.8939	0.1844	137	0.1613	2692	X-RAY DIFFRACTION	100
1.8939-1.9616	0.1859	160	0.159	2632	X-RAY DIFFRACTION	100
1.9616-2.0401	0.1745	133	0.1545	2715	X-RAY DIFFRACTION	100
2.0401-2.133	0.1632	133	0.1553	2675	X-RAY DIFFRACTION	100
2.133-2.2454	0.1602	150	0.1567	2661	X-RAY DIFFRACTION	100
2.2454-2.3861	0.1816	146	0.1623	2690	X-RAY DIFFRACTION	100
2.3861-2.5703	0.1918	136	0.1641	2695	X-RAY DIFFRACTION	100
2.5703-2.8289	0.1777	132	0.1658	2710	X-RAY DIFFRACTION	100
2.8289-3.2381	0.1906	157	0.1733	2690	X-RAY DIFFRACTION	100
3.2381-4.079	0.1586	138	0.1476	2695	X-RAY DIFFRACTION	100
4.079-39.8368	0.1414	136	0.1484	2715	X-RAY DIFFRACTION	99

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	2.4277	-0.5742	0.624	1.6718	-0.1592	0.8408	-0.0701	-0.0037	0.0305	0.207	0.077	-0.0281	0.0125	0.0304	-0.0081	0.0808	0.0146	-0.0055	0.0693	-0.0074	0.0598	-18.4252	-21.2592	3.7806
2	2.8662	-4.6707	0.0455	7.4435	-0.2009	0.1174	-0.1153	-0.051	0.3741	0.3174	0.0484	-0.6545	-0.0386	-0.0229	0.0544	0.1437	0.0031	-0.0011	0.1335	-0.0098	0.1368	1.9355	-13.8651	20.1148
3	1.0792	0.8076	0.1852	3.0552	0.3026	0.7982	0.0384	0.05	0.0136	-0.0318	0.0326	-0.1058	-0.0103	0.0282	-0.0702	0.0647	0.0022	0.0073	0.0793	0.0055	0.0664	-14.5658	-2.8244	-8.1053
4	1.3266	-3.737	0.3951	7.5133	-1.6774	-0.0453	-0.0581	-0.0502	-0.1535	0.1267	0.1105	0.313	-0.0049	-0.0377	-0.0439	0.2246	0.035	-0.0534	0.1408	-0.0223	0.1384	-7.928	-7.4698	16.3852
5	0.8555	1.9135	-1.0826	7.9754	-7.3998	8.7606	0.1471	0.4721	0.0655	-0.2233	0.2723	0.6229	-0.2266	-0.7485	-0.3643	0.0981	-0.0085	-0.0374	0.1566	0.0236	0.1305	-29.6025	-16.6033	-9.4172

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and ((resseq 3:118))
2	X-RAY DIFFRACTION	2	chain 'A' and ((resseq 119:163))
3	X-RAY DIFFRACTION	3	chain 'B' and ((resseq 4:113))
4	X-RAY DIFFRACTION	4	chain 'B' and ((resseq 114:158))
5	X-RAY DIFFRACTION	5	chain 'C' and ((resseq 3:8))

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