PDB-4hkb: CH67 Fab (unbound) from the CH65-67 Lineage

ID or keywords:

Entry

Database: PDB / ID: 4hkb

Title

CH67 Fab (unbound) from the CH65-67 Lineage

Components

CH67 heavy chain
CH67 light chain

Keywords

IMMUNE SYSTEM /

Fab fragment

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.6 Å

Authors

Schmidt, A.G. / Harrison, S.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.
Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T. ...

History

Deposition	Oct 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 5, 2012	Group: Database references
Revision 1.2	Jan 16, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hkb.cif.gz	911.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4hkb.ent.gz	793.3 KB	Display	PDB format
PDBx/mmJSON format	4hkb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hk/4hkb ftp://data.pdbj.org/pub/pdb/validation_reports/hk/4hkb	HTTPS FTP

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Related structure data

Related structure data	4hk0C 4hk3C 4hkxC C: citing same article (ref.)
Similar structure data	1him-1 2gjz-2 3mlt-4 3mlt-3 6kdh-d 5jny-1 1b4j-d 5myk-d 6hgu-1 2w65-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4hk0C

4hk3C

4hkxC

C: citing same article (ref.)

Similar structure data

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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

J: CH67 heavy chain

A: CH67 heavy chain

C: CH67 heavy chain

E: CH67 heavy chain

G: CH67 heavy chain

I: CH67 heavy chain

N: CH67 light chain

B: CH67 light chain

D: CH67 light chain

F: CH67 light chain

H: CH67 light chain

K: CH67 light chain

290 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

J: CH67 heavy chain

N: CH67 light chain

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

2

A: CH67 heavy chain

B: CH67 light chain

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

3

C: CH67 heavy chain

D: CH67 light chain

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

4

E: CH67 heavy chain

F: CH67 light chain

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

5

G: CH67 heavy chain

H: CH67 light chain

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

6

I: CH67 heavy chain

K: CH67 light chain

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

Unit cell

Length a, b, c (Å)	113.249, 123.269, 228.828
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	CH67 heavy chain Mass: 25645.678 Da / Num. of mol.: 6 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody	CH67 light chain Mass: 22671.949 Da / Num. of mol.: 6 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.35 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15-20% PEG4000, 10 mM Tris-HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.97919 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2012

Radiation

Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97919 Å / Relative weight: 1

Reflection

Resolution: 3.6→50 Å / Num. obs: 38632 / % possible obs: 99.8 % / Redundancy: 4.8 % / R_merge(I) obs: 0.107 / Χ²: 1.273 / Net I/σ(I): 6.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.6-3.66	5	0.452	1891	0.855	1	99.9
3.66-3.73	4.9	0.36	1871	1.039	1	100
3.73-3.8	4.9	0.392	1924	0.903	1	99.9
3.8-3.88	5	0.392	1895	0.862	1	100
3.88-3.96	4.9	0.314	1954	0.926	1	99.9
3.96-4.05	5	0.249	1848	0.942	1	100
4.05-4.16	4.9	0.215	1913	0.939	1	99.9
4.16-4.27	4.9	0.185	1942	1.059	1	99.9
4.27-4.39	4.9	0.161	1895	1.141	1	100
4.39-4.54	4.9	0.131	1911	1.253	1	99.9
4.54-4.7	4.9	0.125	1946	1.306	1	99.9
4.7-4.89	4.9	0.116	1904	1.472	1	99.9
4.89-5.11	4.9	0.118	1942	1.494	1	99.9
5.11-5.38	4.8	0.121	1930	1.654	1	99.8
5.38-5.71	4.8	0.111	1925	1.796	1	99.8
5.71-6.15	4.8	0.114	1938	1.668	1	99.8
6.15-6.77	4.7	0.094	1964	1.327	1	99.7
6.77-7.75	4.6	0.071	1963	1.289	1	99.8
7.75-9.75	4.7	0.049	1989	1.676	1	99.5
9.75-50	4.4	0.039	2087	1.938	1	98.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.6→41.698 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7468 / SU ML: 0.37 / σ(F): 0 / Phase error: 31.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3056	1846	5.14 %
R_work	0.2583	-	-
obs	0.2608	35922	94.88 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.383 Å² / k_sol: 0.237 e/Å³

Displacement parameters

B_iso max: 371.71 Å² / B_iso mean: 122.4034 Å² / B_iso min: 20 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.4352 Å²	-0 Å²	-0 Å²
2-	-	-0.9282 Å²	0 Å²
3-	-	-	-8.507 Å²

Refinement step

Cycle: LAST / Resolution: 3.6→41.698 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17971	0	0	0	17971

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	18440
X-RAY DIFFRACTION	f_angle_d	1.378	25132
X-RAY DIFFRACTION	f_chiral_restr	0.057	2854
X-RAY DIFFRACTION	f_plane_restr	0.008	3215
X-RAY DIFFRACTION	f_dihedral_angle_d	12.33	6470

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.6-3.6973	0.3755	141	0.3418	2596	2737	95
3.6973-3.8061	0.3282	121	0.3188	2503	2624	91
3.8061-3.9288	0.3358	150	0.3026	2417	2567	90
3.9288-4.0691	0.3709	133	0.2774	2464	2597	91
4.0691-4.2319	0.3213	137	0.2612	2559	2696	94
4.2319-4.4243	0.3334	137	0.2412	2608	2745	95
4.4243-4.6573	0.2579	140	0.2106	2612	2752	95
4.6573-4.9486	0.2346	143	0.2137	2666	2809	97
4.9486-5.33	0.2655	141	0.2179	2642	2783	96
5.33-5.8651	0.2722	143	0.2357	2685	2828	97
5.8651-6.7107	0.3213	153	0.2853	2691	2844	97
6.7107-8.4433	0.3828	154	0.2767	2768	2922	99
8.4433-41.7012	0.2815	153	0.2588	2865	3018	97

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	1.6661	-0.8021	-0.7483	2.347	2.9509	3.3191	-0.2342	0.0026	0.2341	0.3563	0.2416	0.0353	-0.0902	-0.3498	0.0103	0.5496	-0.0466	-0.0015	0.5548	0.0045	0.4471	-41.2964	19.5248	-24.9884
2	3.1926	0.2653	-1.4285	1.5586	-1.0069	1.1241	-0.4215	0.6878	-0.9606	-0.2815	0.8735	-0.3524	0.4677	-0.6256	-0.0211	0.8766	-0.005	-0.0877	1.071	-0.2812	1.0018	-41.308	-8.1125	-51.3828
3	2.1277	-1.7479	-0.6148	3	0.8742	2.4143	-0.3481	0.1698	-0.4614	0.4116	-0.2743	-0.4173	0.7838	0.5997	-0.0415	1.0547	-0.0761	0.0294	0.5407	0.0546	0.5089	-47.16	3.2263	-12.3124
4	3.8546	0.0842	1.0405	2.2348	0.6616	2.2311	1.1607	-0.3085	-1.479	0.255	-0.5447	-1.3624	0.3362	-0.0359	0.5739	0.8481	0.0809	-0.1935	0.4778	-0.0891	1.7223	-33.3396	-17.4692	-40.1765
5	3.6786	-1.0422	0.3507	2.1518	-0.7778	3.4797	-0.4922	0.1409	0.0624	0.4655	0.1446	0.5863	0.3609	-0.2402	-0.0197	0.466	-0.0129	0.0531	0.4903	-0.0356	0.5921	-42.7389	47.9359	-32.9527
6	1.4547	-1.3927	-1.2713	1.5279	0.8533	1.672	0.2004	-1.5685	0.5522	0.8477	-0.1637	0.3261	0.1545	-0.3497	0.1136	1.0029	-0.1444	0.3463	1.4868	-0.0332	0.5529	-42.4144	39.3745	4.6269
7	1.4136	-0.5071	0.3797	2.1107	1.2127	2.3732	-0.3937	-0.3704	0.5228	0.1328	0.2725	-0.174	-0.8381	0.081	-0.0646	1.0494	0.1455	-0.0798	0.6057	-0.0925	0.946	-45.3427	67.7495	-25.053
8	2.5643	-1.216	-0.728	1.0376	-0.8318	2.5349	-0.2187	-1.3489	1.444	0.0931	1.0557	-0.7023	-0.1589	-0.5357	0.3919	0.8674	-0.0632	-0.0839	1.2945	-0.587	1.0151	-35.7361	52.8798	4.931
9	2.796	2.308	-0.5544	5.4315	-0.148	3.5531	-0.0872	-0.1401	0.0972	0.0527	-0.2025	0.3089	0.0671	-0.3952	-0.0132	0.3305	-0.0369	-0.1493	0.6092	-0.0451	0.452	-48.6824	27.0472	-53.0925
10	1.6173	0.0907	0.4538	1.8751	-0.2201	2.0668	-0.0876	0.0587	0.3576	-0.7388	0.7007	-0.3872	-1.8343	-0.8578	0.0302	1.6103	0.1587	0.0964	1.0535	-0.2028	1.2137	-43.7455	62.4907	-66.7425
11	3.1823	1.7032	1.2397	0.9468	0.4626	4.5156	-0.1422	0.4667	0.5034	-1.6742	0.0964	0.3765	0.5368	0.7978	-0.3382	1.0374	-0.0642	-0.4873	0.7767	-0.0804	0.7311	-53.0726	23.3683	-73.8169
12	3.7908	0.8745	2.0681	4.37	-0.4459	2.6244	0.454	0.6103	0.8297	0.0341	0.2839	0.0956	-1.2963	1.2513	0.0224	1.4394	-0.2246	0.2355	1.4573	-0.246	0.7792	-36.6113	55.0352	-79.0536
13	2.6973	2.9662	0.4674	3.8869	0.7845	2.5475	0.1167	-0.2034	-0.5707	0.0562	-0.381	-0.5494	0.1019	0.2452	-0.0315	0.328	-0.044	-0.0988	0.4646	0.1586	0.5582	-14.2303	33.7963	-53.2429
14	0.8342	0.4183	0.0034	1.073	-0.0664	1.5727	-0.8468	0.0882	-1.5116	0.7504	0.1967	0.5703	1.9739	-0.2999	0.1297	1.7963	0.1891	1.0065	0.9266	0.095	1.874	-17.919	-2.3838	-67.3426
15	1.4424	-0.2818	-0.6849	1.8463	0.843	3.1908	-0.0088	0.7353	-0.0628	-1.6228	0.0629	-0.2188	-0.0043	-0.3947	-0.0084	1.0006	-0.0659	0.1477	0.7334	0.0112	0.8229	-9.653	37.3317	-73.9981
16	0.8096	0.1153	-1.3273	1.4423	0.2431	1.9287	0.4234	1.3446	-1.1833	-0.5712	0.359	0.4116	0.3481	-1.5586	-0.0287	1.1439	-0.1987	0.0465	1.4611	0.085	1.4218	-24.8779	3.9738	-79.521
17	3.2028	-0.8334	-0.3953	2.4867	0.9156	4.1142	-0.2882	0.1962	0.0387	-0.3744	0.3104	-0.2913	-0.3064	0.4787	-0.0035	0.4795	0.0408	-0.0054	0.5923	-0.0836	0.4474	-7.8012	12.8046	-32.5667
18	2.0157	-0.4881	0.6974	0.6387	0.5784	1.2065	-0.7391	-0.7237	1.2167	0.6561	-0.3608	0.0266	-1.3779	0.1308	0.0757	1.3405	-0.1009	-0.5035	1.3869	0.131	0.9695	-8.5153	21.4433	4.7584
19	2.598	0.24	-1.039	4.3589	-1.1994	2.4944	-0.1068	0.1186	-0.6441	1.2158	-0.0306	0.3874	1.9522	-0.1392	-0.1284	1.1489	0.2546	0.0022	0.6054	-0.103	0.9629	-4.6877	-7.0032	-24.9771
20	5.6826	-0.3353	0.8143	1.5824	0.6416	2.9183	0.3827	-1.3949	-1.5499	0.6704	0.434	0.9819	0.2455	-0.5675	0.9119	1.3476	0.2211	0.4057	1.7995	0.5989	1.0843	-16.8842	7.6764	5.8139
21	2.5719	-1.1992	0.568	1.6997	-0.9224	3.924	-0.2347	-0.0502	0.0838	0.0453	0.1681	-0.0833	0.1694	0.248	0.0064	0.5894	-0.1684	-0.091	0.5231	-0.0444	0.4615	-9.4844	41.0328	-24.6698
22	2.6773	-0.5981	1.2115	2.9934	-1.1982	1.5558	-0.2048	0.3133	0.7273	-0.9594	0.2285	-0.1459	0.5206	0.278	-0.0076	0.8758	-0.2308	0.0443	0.7223	0.0366	0.9265	-8.319	68.0203	-51.3411
23	2.2596	-0.5442	0.9316	5.0508	1.3684	0.9722	-0.0958	-1.0415	0.6433	1.3173	-0.3724	0.8862	-0.7512	0.0538	-0.1178	0.9162	-0.4709	-0.2904	0.8054	-0.304	0.5995	-4.2562	57.3716	-11.7777
24	2.2233	0.7275	0.0479	1.992	-0.0485	1.5328	0.1204	-0.532	1.1714	-0.0944	-0.2764	1.5278	-0.3097	-0.1384	-0.072	0.7778	-0.3261	0.0532	0.3266	-0.1353	1.5855	-15.9331	77.0573	-40.9581

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'J' and ( resseq 1:128 )	J	1 - 128
2	X-RAY DIFFRACTION	2	chain 'J' and ( resseq 129:226 )	J	129 - 226
3	X-RAY DIFFRACTION	3	chain 'N' and ( resseq 2:110 )	N	2 - 110
4	X-RAY DIFFRACTION	4	chain 'N' and ( resseq 111:210 )	N	111 - 210
5	X-RAY DIFFRACTION	5	chain 'A' and ( resseq 1:128 )	A	1 - 128
6	X-RAY DIFFRACTION	6	chain 'A' and ( resseq 129:226 )	A	129 - 226
7	X-RAY DIFFRACTION	7	chain 'B' and ( resseq 2:110 )	B	2 - 110
8	X-RAY DIFFRACTION	8	chain 'B' and ( resseq 111:205 )	B	111 - 205
9	X-RAY DIFFRACTION	9	chain 'C' and ( resseq 1:128 )	C	1 - 128
10	X-RAY DIFFRACTION	10	chain 'C' and ( resseq 129:225 )	C	129 - 225
11	X-RAY DIFFRACTION	11	chain 'D' and ( resseq 2:110 )	D	2 - 110
12	X-RAY DIFFRACTION	12	chain 'D' and ( resseq 111:205 )	D	111 - 205
13	X-RAY DIFFRACTION	13	chain 'E' and ( resseq 1:128 )	E	1 - 128
14	X-RAY DIFFRACTION	14	chain 'E' and ( resseq 129:226 )	E	129 - 226
15	X-RAY DIFFRACTION	15	chain 'F' and ( resseq 2:110 )	F	2 - 110
16	X-RAY DIFFRACTION	16	chain 'F' and ( resseq 111:203 )	F	111 - 203
17	X-RAY DIFFRACTION	17	chain 'G' and ( resseq 1:128 )	G	1 - 128
18	X-RAY DIFFRACTION	18	chain 'G' and ( resseq 129:226 )	G	129 - 226
19	X-RAY DIFFRACTION	19	chain 'H' and ( resseq 3:109 )	H	3 - 109
20	X-RAY DIFFRACTION	20	chain 'H' and ( resseq 110:207 )	H	110 - 207
21	X-RAY DIFFRACTION	21	chain 'I' and ( resseq 1:128 )	I	1 - 128
22	X-RAY DIFFRACTION	22	chain 'I' and ( resseq 129:226 )	I	129 - 226
23	X-RAY DIFFRACTION	23	chain 'K' and ( resseq 2:109 )	K	2 - 109
24	X-RAY DIFFRACTION	24	chain 'K' and ( resseq 110:210 )	K	110 - 210

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Yorodumi