PDB-7dun: Crystal structure of Fab fragment of Daratumumab

ID or keywords:

Entry

Database: PDB / ID: 7dun

Title

Crystal structure of Fab fragment of Daratumumab

Components

Fab heavy chainFragment antigen-binding
Fab light chainFragment antigen-binding

Keywords

ANTITUMOR PROTEIN /

CD38 /

Daratumumab /

multiple myeloma

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.607 Å

Authors

Yu, X.J. / Wang, L. / Yu, C.F.

Citation

Journal: To Be Published
Title: Crystal structure of Fab fragment of Daratumumab
Authors: Yu, X.J. / Wang, L. / Yu, C.F.

History

Deposition	Jan 10, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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	7dun.cif.gz	191.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7dun.ent.gz	151.5 KB	Display	PDB format
PDBx/mmJSON format	7dun.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/du/7dun ftp://data.pdbj.org/pub/pdb/validation_reports/du/7dun	HTTPS FTP

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Related structure data

Related structure data	4cmhS S: Starting model for refinement
Similar structure data	1kfa-2 6wla-1 3eo0-2 4xbg-4 5h2b-d 1ngx-2 6pds-1 1kfa-1 4ouu-1 5nyx-2 7k8n-d 4r7n-5 5jw5-2 6ev1-6 4r4b-4 1uwe-3 6z3k-9 5i76-1 3fo0-d 5b6f-1 Search similar-shape structures by Omokage search (details)

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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

H: Fab heavy chain

L: Fab light chain

46.8 kDa, 2 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)	89.905, 89.905, 217.477
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	H-510- HOH

#1: Antibody	Fab heavy chain / Fragment antigen-binding Mass: 23595.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Fab light chain / Fragment antigen-binding Mass: 23173.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 520 / 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: evaporation, recrystallization Details: 0.2M Potassium phosphate monobasic, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 23, 2020
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 68212 / % possible obs: 100 % / Redundancy: 17 % / CC_1/2: 0.996 / R_merge(I) obs: 0.1 / Net I/σ(I): 30.5
Reflection shell	Resolution: 1.6→1.64 Å / Num. unique obs: 68212 / CC_1/2: 0.996

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.14_3260	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4cmh

4cmh

Resolution: 1.607→31.258 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2179	3045	2.93 %
R_work	0.2052	66212	-
obs	0.2056	68212	99.76 %

Solvent computation

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

Displacement parameters

B_iso max: 76.2 Å² / B_iso mean: 29.1244 Å² / B_iso min: 11.86 Å²

Refinement step

Cycle: final / Resolution: 1.607→31.258 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3270	0	0	520	3790
B_iso mean	-	-	-	33.65	-
Num. residues	-	-	-	-	432

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.607-1.6472	0.2688	135	0.2686	4468	97
1.6472-1.6917	0.2723	141	0.2459	4680	100
1.6917-1.7415	0.2293	141	0.2328	4645	100
1.7415-1.7977	0.2483	141	0.2228	4678	100
1.7977-1.8619	0.2115	140	0.2199	4643	100
1.8619-1.9365	0.2205	141	0.218	4671	100
1.9365-2.0246	0.2203	142	0.2133	4705	100
2.0246-2.1313	0.2399	142	0.2147	4694	100
2.1313-2.2648	0.2364	143	0.2155	4730	100
2.2648-2.4396	0.2165	143	0.2214	4733	100
2.4396-2.685	0.2195	144	0.2269	4760	100
2.685-3.0732	0.2789	145	0.2119	4788	100
3.0732-3.8708	0.1838	147	0.1796	4868	100
3.8708-31.25	0.1975	155	0.1857	5149	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	1.7087	-0.7658	-0.4343	1.6858	0.1636	1.4671	0.0274	0.0097	-0.0256	-0.0138	-0.0291	0.0036	-0.0137	0.0316	0.054	0.1384	0.006	0.0145	0.133	0.0144	0.1451	38.5101	49.9871	90.4207
2	0.6709	-0.0529	0.0635	0.7018	-0.139	0.549	-0.3128	-0.2422	-0.8953	0.1147	-0.0334	-0.2238	0.4983	-0.121	0.3674	0.5197	-0.0189	0.1662	0.3825	-0.0065	0.4958	25.6842	20.5487	102.8842
3	1.9767	0.0046	-0.6465	0.8497	-0.2495	1.3182	-0.2661	0.2892	-0.5229	-0.3197	0.0164	-0.1152	0.5158	-0.219	0.1894	0.4468	-0.0699	0.1327	0.2976	-0.0672	0.3708	20.9906	25.3825	100.3158
4	2.0893	-0.332	-1.3096	0.2491	0.1343	1.1729	0.0707	-0.1869	0.0913	0.127	-0.057	-0.0141	0.0418	0.1711	-0.0837	0.169	0.0009	0.0089	0.1659	0.0018	0.1469	28.5616	57.8849	114.5684
5	1.7162	-0.0164	-0.4039	0.884	0.0438	1.7579	-0.0742	0.0836	0.0968	-0.171	0.0429	-0.0228	-0.1461	-0.1437	-0.0515	0.1722	0.0066	0.0197	0.1426	0.0028	0.145	27.1253	60.6784	102.3903
6	5.8316	2.6597	-0.6776	1.9509	-0.3379	0.6353	0.106	-0.2261	0.3616	0.0276	-0.0709	0.0712	-0.2869	0.0883	-0.1104	0.2173	0.0105	0.0203	0.172	-0.0247	0.1939	27.2949	65.4834	110.3069
7	1.7852	-0.1574	-1.4031	1.445	-0.2071	2.3894	-0.1007	0.0087	-0.1389	0.0058	-0.0135	0.0757	0.0955	-0.074	0.0157	0.1808	-0.0034	0.0152	0.1112	-0.0084	0.1427	23.3256	54.1586	107.9726
8	2.6518	0.0988	-1.4746	1.3112	-0.5313	2.4482	0.0018	-0.1665	0.058	-0.1148	-0.0819	-0.3865	-0.0067	0.327	0.0386	0.181	-0.0208	0.0337	0.1762	-0.0082	0.1934	39.8589	60.363	102.1006
9	0.6702	0.3721	-0.4389	0.5119	-0.6374	0.7571	0.0264	-0.109	-0.1912	-0.05	-0.0917	-0.0156	0.0981	-0.0222	0.0895	0.2245	-0.0164	0.0313	0.1628	0.0056	0.2239	16.803	37.6568	116.5683
10	1.4295	-0.9411	-0.5143	1.4355	-0.0199	0.6533	-0.1011	-0.0634	-0.3598	-0.3568	0.0058	-0.3003	0.3396	0.2164	0.1551	0.3849	0.003	0.1014	0.229	0.0157	0.3939	22.4588	22.488	114.6498
11	0.0114	0.0432	-0.0732	1.694	-1.3901	1.305	-0.0844	-0.3783	-0.3879	0.1346	0.0604	-0.3617	0.2306	0.1903	0.2497	0.3824	0.0595	0.0476	0.4357	0.1032	0.52	28.0986	21.3428	120.745
12	0.9507	-0.439	-0.4964	1.4821	0.377	0.8382	-0.1273	-0.0925	-0.3145	-0.3088	-0.0098	-0.2733	0.4061	0.156	0.1641	0.365	0.0173	0.0945	0.2082	0.0372	0.3547	22.2348	23.6748	115.5027
13	1.4642	-1.0567	-0.6429	2.0431	0.7019	1.6034	-0.117	-0.1312	-0.4794	-0.0532	0.0476	-0.0287	0.4142	-0.0621	0.2524	0.3091	-0.0546	0.0381	0.2286	0.0489	0.3346	15.2666	22.656	123.1823

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 120 )	H	1 - 120
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 121 through 143 )	H	121 - 143
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 144 through 223 )	H	144 - 223
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 25 )	L	1 - 25
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 26 through 61 )	L	26 - 61
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 62 through 75 )	L	62 - 75
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 76 through 90 )	L	76 - 90
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 91 through 101 )	L	91 - 101
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 102 through 118 )	L	102 - 118
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 119 through 150 )	L	119 - 150
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 151 through 163 )	L	151 - 163
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 164 through 197 )	L	164 - 197
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 198 through 212 )	L	198 - 212

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