PDB-6w4w: Crystal Structure of the Fab fragment of humanized 5c8 antibody

ID or keywords:

Entry

Database: PDB / ID: 6w4w

Title

Crystal Structure of the Fab fragment of humanized 5c8 antibody

Components

5c8 Fab heavy chain
5c8 Fab light chain

Keywords

IMMUNE SYSTEM / immunoglobulin / Fab

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.77 Å

Authors

Henderson, J.N. / Mills, J.H. / Simmons, C.R.

Citation

Journal: Biochemistry / Year: 2020
Title: Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.
Authors: Henderson, J.N. / Simmons, C.R. / Fahmi, N.E. / Jeffs, J.W. / Borges, C.R. / Mills, J.H.

History

Deposition	Mar 11, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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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Download

PDBx/mmCIF format	6w4w.cif.gz	182.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6w4w.ent.gz	143.1 KB	Display	PDB format
PDBx/mmJSON format	6w4w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6w4w_validation.pdf.gz	425.4 KB	Display	wwPDB validaton report
Full document	6w4w_full_validation.pdf.gz	426.3 KB	Display
Data in XML	6w4w_validation.xml.gz	19.3 KB	Display
Data in CIF	6w4w_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w4/6w4w ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w4w	HTTPS FTP

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Related structure data

Related structure data	6bjzC 6w5aC 6w9gC 1i9rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ygv-2 5mu2-1 4yhk-d 6med-2 4yhn-1 1mj7-d 5t6p-2 5vr9-1 3inu-2 6cdm-2 3gnm-d 4r7n-3 5etu-1 5t1k-2 4dn3-d 1iqw-d 5dq9-1 6w5a-d 2uyl-1 4kk8-3 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

L: 5c8 Fab light chain

H: 5c8 Fab heavy chain

48 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)	90.894, 60.305, 73.456
Angle α, β, γ (deg.)	90.000, 96.270, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	L-432- HOH

#1: Antibody	5c8 Fab light chain Mass: 23881.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	5c8 Fab heavy chain Mass: 24078.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.09 Å³/Da / Density % sol: 41.04 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, sitting drop Details: 33% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 4.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97934 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 1.77→50.16 Å / Num. obs: 38013 / % possible obs: 98.1 % / Redundancy: 6.3 % / R_merge(I) obs: 0.052 / R_pim(I) all: 0.022 / R_rim(I) all: 0.057 / Χ²: 0.874 / Net I/σ(I): 11.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.77-1.8	5.6	0.324	1790	0.936	0.143	0.356	0.523	94.4
1.8-1.83	6.1	0.289	1878	0.961	0.123	0.315	0.543	95.9
1.83-1.87	6.2	0.246	1882	0.974	0.104	0.268	0.584	98.8
1.87-1.91	6.1	0.204	1866	0.976	0.087	0.222	0.637	96.8
1.91-1.95	6	0.179	1911	0.981	0.077	0.196	0.651	97.4
1.95-1.99	6	0.15	1854	0.988	0.065	0.164	0.754	97.9
1.99-2.04	5.6	0.137	1856	0.987	0.062	0.151	0.828	96.7
2.04-2.1	5.9	0.121	1925	0.991	0.053	0.132	0.836	98.6
2.1-2.16	6.4	0.105	1903	0.994	0.044	0.114	0.88	99.1
2.16-2.23	6.4	0.094	1895	0.995	0.039	0.102	0.918	99.4
2.23-2.31	6.3	0.089	1935	0.996	0.038	0.097	1.013	99.1
2.31-2.4	6.3	0.083	1890	0.995	0.036	0.091	1.018	98.4
2.4-2.51	5.9	0.075	1894	0.995	0.033	0.082	1.058	97.1
2.51-2.64	6.8	0.067	1923	0.997	0.027	0.072	1.025	99.6
2.64-2.81	6.8	0.058	1925	0.998	0.024	0.063	1.074	99.6
2.81-3.03	6.6	0.052	1928	0.998	0.022	0.057	1.059	98.9
3.03-3.33	6.1	0.046	1891	0.998	0.02	0.05	1.004	97.8
3.33-3.81	7	0.04	1953	0.999	0.016	0.043	0.959	99.3
3.81-4.8	6.3	0.031	1919	0.999	0.013	0.034	1	98.5
4.8-50	6.5	0.03	1995	0.999	0.012	0.032	0.928	98.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	6.69 Å	42.56 Å
Translation	6.69 Å	42.56 Å

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHASER	2.6.1	phasing
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1i9r

1i9r

Resolution: 1.77→50.16 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.951 / SU B: 4.987 / SU ML: 0.08 / SU R Cruickshank DPI: 0.122 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2042	1853	4.9 %	RANDOM
R_work	0.1693	-	-	-
obs	0.171	36102	98.24 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 63.19 Å² / B_iso mean: 24.955 Å² / B_iso min: 11.13 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	0.05 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: final / Resolution: 1.77→50.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3205	0	0	271	3476
B_iso mean	-	-	-	30.42	-
Num. residues	-	-	-	-	434

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	3320
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2959
X-RAY DIFFRACTION	r_angle_refined_deg	1.758	1.945	4544
X-RAY DIFFRACTION	r_angle_other_deg	0.953	3.001	6849
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.671	5.022	445
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.406	24.833	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.34	15	489
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.575	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	521
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	3818
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	726

LS refinement shell

Resolution: 1.77→1.816 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.223	126	-
R_work	0.2	2607	-
all	-	2733	-
obs	-	-	96.5 %

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	3.1652	1.5501	-1.8832	3.2205	-2.4455	4.9906	0.0268	0.2612	0.1943	-0.0482	0.0777	0.2118	0.0226	-0.262	-0.1045	0.0816	0.0052	-0.0302	0.1298	0.0727	0.118	-0.8796	7.4562	82.9424
2	4.9588	1.7501	-4.3143	1.6207	-3.3714	7.2221	-0.0304	-0.2103	-0.134	0.0479	-0.1301	-0.0923	-0.0103	0.307	0.1605	0.0964	0.0046	-0.0369	0.0761	0.0032	0.0841	21.0443	-7.3763	117.7273
3	2.931	-0.0675	0.1282	2.1403	-0.8248	6.1864	-0.0258	0.3331	0.0364	-0.2057	0.0732	0.0164	0.3191	-0.0452	-0.0474	0.055	-0.0187	-0.0014	0.0882	-0.0135	0.0448	9.3882	2.6321	78.3288
4	2.4404	0.6287	-1.0341	1.1555	-0.3413	3.3799	-0.0551	0.3445	-0.0797	-0.1218	0.0656	0.0863	0.2611	-0.1354	-0.0105	0.0676	-0.0083	-0.0261	0.0898	0.0003	0.0347	5.1278	1.7061	80.5782
5	4.2017	0.5462	2.3565	1.1128	0.8831	2.8227	-0.0316	0.0275	0.0809	0.1091	0.0228	-0.0461	-0.0425	0.1526	0.0088	0.0279	-0.0102	-0.0045	0.0167	0.0029	0.0166	5.6211	3.2827	115.7692
6	2.1239	-0.0971	-2.2552	1.7734	-1.1657	10.0292	0.0238	-0.1163	0.1142	0.1632	-0.0136	0.0599	-0.231	-0.1256	-0.0102	0.078	-0.031	-0.0004	0.0356	-0.0201	0.0479	5.3566	13.5829	124.0033
7	3.544	2.4698	1.9293	4.5404	3.9605	6.9961	-0.0263	0.1686	-0.0469	-0.1117	0.0048	-0.1282	-0.0344	0.0594	0.0215	0.0226	0.003	0.0065	0.0164	0.0141	0.0489	3.3319	1.6865	103.8786
8	2.9853	1.4337	2.8274	1.3594	2.122	4.1664	0.0861	-0.4557	0.1881	0.2482	-0.1227	0.0529	0.1602	-0.2148	0.0365	0.1189	-0.0224	0.0029	0.1127	-0.0365	0.05	5.2558	6.92	124.9904
9	4.5734	0.0453	-0.1031	4.1333	6.0847	8.9678	0.0079	0.1847	-0.1395	0.3298	0.1553	-0.1198	0.4861	0.2426	-0.1632	0.1405	0.0193	-0.0067	0.0629	0.0343	0.0504	27.7373	1.4234	91.0142
10	4.7873	0.5546	-0.1024	3.9453	1.5662	5.5839	-0.1193	0.3707	0.1887	-0.2169	-0.0913	0.2093	-0.3497	-0.0381	0.2107	0.0683	-0.0293	-0.038	0.0732	0.0312	0.0331	20.2801	9.8759	83.3075
11	4.8303	-2.1245	0.5746	6.1847	1.3962	3.0215	-0.1007	0.7252	0.3221	-0.3714	-0.104	-0.3113	-0.4042	0.5199	0.2047	0.1486	-0.0917	0.0279	0.2963	0.0928	0.0873	30.2466	9.9909	77.2085
12	4.3609	0.479	0.5676	3.9428	2.2178	4.8161	-0.1115	0.3045	0.1671	-0.1815	0.066	-0.0484	-0.2996	0.3079	0.0456	0.0512	-0.022	-0.0102	0.0531	0.0256	0.0173	26.6244	9.5096	86.3741
13	1.1361	0.0872	-0.4981	0.6824	-0.2057	1.7729	0.0298	0.0535	-0.004	-0.045	-0.0342	-0.0997	-0.0964	0.1946	0.0044	0.0284	-0.006	-0.0141	0.039	-0.0061	0.0469	22.9278	5.8586	97.433
14	1.3967	1.1219	-0.5022	3.0105	-0.8903	1.1812	0.0576	-0.1473	-0.0819	0.1394	-0.0658	-0.0226	0.0265	0.1577	0.0082	0.0283	0.0059	-0.0197	0.0363	0.0015	0.0331	15.1583	-1.8927	111.7978
15	8.4215	1.82	-5.7133	9.7459	-4.5312	8.2209	-0.1346	-0.1804	-0.5162	-0.4109	-0.0092	-0.3077	0.1541	0.4679	0.1438	0.0427	0.0012	-0.0131	0.1709	0.0072	0.126	28.9829	3.0535	104.4039
16	3.3991	0.0946	0.5326	4.2178	3.6047	4.988	0.0301	0.4969	-0.2455	0.0266	0.1249	-0.1235	0.1438	0.4747	-0.155	0.0357	0.0171	-0.0078	0.1403	-0.0396	0.0907	31.1948	4.4357	85.9062

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	L	2 - 26
2	X-RAY DIFFRACTION	2	H	212 - 219
3	X-RAY DIFFRACTION	3	L	27 - 51
4	X-RAY DIFFRACTION	4	L	52 - 110
5	X-RAY DIFFRACTION	5	L	111 - 151
6	X-RAY DIFFRACTION	6	L	152 - 165
7	X-RAY DIFFRACTION	7	L	166 - 179
8	X-RAY DIFFRACTION	8	L	180 - 215
9	X-RAY DIFFRACTION	9	H	3 - 10
10	X-RAY DIFFRACTION	10	H	33 - 50
11	X-RAY DIFFRACTION	11	H	51 - 76
12	X-RAY DIFFRACTION	12	H	77 - 100
13	X-RAY DIFFRACTION	13	H	101 - 130
14	X-RAY DIFFRACTION	14	H	131 - 203
15	X-RAY DIFFRACTION	15	H	204 - 211
16	X-RAY DIFFRACTION	16	H	11 - 32

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