PDB-6oc7: HMP42 Fab in complex with Protein G

ID or keywords:

Entry

Database: PDB / ID: 6oc7

Title

HMP42 Fab in complex with Protein G

Components

Heavy chain of HMP42 Fab
Immunoglobulin G-binding protein G
Light chain for HMP42 Fab

Keywords

IMMUNE SYSTEM / Anti-HIV antibody / Fab fragment / crystallization chaperone

Function / homology

Function and homology information

IgG binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Streptococcus sp. group G (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.296 Å

Authors

Bernard, S.M. / Wilson, I.A.

Funding support

United States, 1items

Citation

Journal: Science / Year: 2019
Title: A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.
Authors: Jon M Steichen / Ying-Cing Lin / Colin Havenar-Daughton / Simone Pecetta / Gabriel Ozorowski / Jordan R Willis / Laura Toy / Devin Sok / Alessia Liguori / Sven Kratochvil / Jonathan L Torres ...
Abstract: Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for ...

History

Deposition	Mar 22, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oc7.cif.gz	216.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6oc7.ent.gz	170.5 KB	Display	PDB format
PDBx/mmJSON format	6oc7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6oc7_validation.pdf.gz	249.4 KB	Display	wwPDB validaton report
Full document	6oc7_full_validation.pdf.gz	249.3 KB	Display
Data in XML	6oc7_validation.xml.gz	947 B	Display
Data in CIF	6oc7_validation.cif.gz	9.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/6oc7 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6oc7	HTTPS FTP

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Related structure data

Related structure data	7875C 7876C 7884C 7885C 6dfgC 6dfhC 6nf5C 6nfcC 4fqqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2qvh-d 5gry-d 3qcb-d 1rq2-d 3qce-d 6h2g-d 6jis-1 2pn0-d 3glu-1 6g3t-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&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

H: Heavy chain of HMP42 Fab

L: Light chain for HMP42 Fab

C: Immunoglobulin G-binding protein G

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	91.132, 54.388, 103.081
Angle α, β, γ (deg.)	90.00, 90.01, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	H-604- HOH
2	1	H-622- HOH

#1: Antibody	Heavy chain of HMP42 Fab Mass: 25196.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Light chain for HMP42 Fab Mass: 22774.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody	Immunoglobulin G-binding protein G / IgG-binding protein G Mass: 7348.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.31 Å³/Da / Density % sol: 46.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 17% PEG 4000, 15% glycerol, 8.5% 2-propanol and 85 mM HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.296→48.103 Å / Num. obs: 120493 / % possible obs: 95.9 % / Redundancy: 3.1 % / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.296→1.37 Å / Num. unique obs: 16114

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4fqq

4fqq

Resolution: 1.296→48.103 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.66

	R_factor	Num. reflection	% reflection
R_free	0.184	6005	4.98 %
R_work	0.1678	-	-
obs	0.1686	120481	96.23 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.296→48.103 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3687	0	0	755	4442

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3815
X-RAY DIFFRACTION	f_angle_d	1.067	5215
X-RAY DIFFRACTION	f_dihedral_angle_d	17.025	1374
X-RAY DIFFRACTION	f_chiral_restr	0.095	595
X-RAY DIFFRACTION	f_plane_restr	0.007	663

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 (%)
1.2955-1.3102	0.4516	124	0.4356	2497	X-RAY DIFFRACTION	64
1.3102-1.3257	0.4207	148	0.4027	3074	X-RAY DIFFRACTION	76
1.3257-1.3418	0.38	172	0.3771	3214	X-RAY DIFFRACTION	82
1.3418-1.3588	0.3788	221	0.3571	3428	X-RAY DIFFRACTION	87
1.3588-1.3767	0.329	218	0.3411	3573	X-RAY DIFFRACTION	92
1.3767-1.3956	0.3204	204	0.2946	3866	X-RAY DIFFRACTION	97
1.3956-1.4155	0.2596	163	0.2698	3895	X-RAY DIFFRACTION	98
1.4155-1.4366	0.2732	211	0.2379	3891	X-RAY DIFFRACTION	99
1.4366-1.4591	0.2186	212	0.2212	3893	X-RAY DIFFRACTION	99
1.4591-1.483	0.2276	213	0.1978	3934	X-RAY DIFFRACTION	99
1.483-1.5086	0.2142	217	0.1917	3925	X-RAY DIFFRACTION	99
1.5086-1.536	0.2011	205	0.1741	3882	X-RAY DIFFRACTION	99
1.536-1.5656	0.1899	237	0.1729	3906	X-RAY DIFFRACTION	100
1.5656-1.5975	0.2063	201	0.1661	3951	X-RAY DIFFRACTION	100
1.5975-1.6322	0.1802	189	0.1645	3914	X-RAY DIFFRACTION	100
1.6322-1.6702	0.1948	208	0.1661	3961	X-RAY DIFFRACTION	100
1.6702-1.712	0.191	165	0.1644	3989	X-RAY DIFFRACTION	100
1.712-1.7583	0.1883	222	0.1606	3937	X-RAY DIFFRACTION	100
1.7583-1.81	0.173	199	0.1614	3998	X-RAY DIFFRACTION	100
1.81-1.8684	0.1923	195	0.1564	3914	X-RAY DIFFRACTION	100
1.8684-1.9352	0.1854	247	0.1544	3917	X-RAY DIFFRACTION	100
1.9352-2.0127	0.1569	190	0.148	3979	X-RAY DIFFRACTION	100
2.0127-2.1043	0.1613	209	0.1453	3955	X-RAY DIFFRACTION	100
2.1043-2.2153	0.1774	202	0.1522	3962	X-RAY DIFFRACTION	100
2.2153-2.354	0.1733	240	0.1613	3931	X-RAY DIFFRACTION	100
2.354-2.5358	0.1864	176	0.1663	4036	X-RAY DIFFRACTION	100
2.5358-2.791	0.1919	192	0.1717	3976	X-RAY DIFFRACTION	100
2.791-3.1947	0.1789	186	0.1601	4017	X-RAY DIFFRACTION	100
3.1947-4.0247	0.1615	226	0.1444	3986	X-RAY DIFFRACTION	100
4.0247-48.1361	0.1353	213	0.1419	4075	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	0.5771	0.0732	-0.3352	0.8819	0.0368	1.2229	-0.0328	0.0661	0.0568	-0.0584	0.0449	-0.0497	-0.0165	0.041	0.0002	0.0835	0.0015	-0.0019	0.1136	0.0165	0.1475	96.1121	46.8438	20.1127
2	1.2822	-0.3229	-0.8774	0.8028	-0.2357	1.4946	0.0058	0.1793	0.166	0.0319	0.1269	0.0785	-0.088	-0.1463	-0.0519	0.0992	0.0044	-0.0034	0.1231	0.021	0.1572	89.7627	50.2476	25.4066
3	2.5236	-0.2685	-0.1053	2.1962	0.2966	1.9524	-0.117	0.086	-0.053	-0.1877	0.154	-0.1891	0.2969	0.2774	-0.0182	0.1392	0.0036	0.019	0.1089	0.0099	0.1541	99.2686	38.292	19.0531
4	0.5612	-0.0356	-0.5194	0.1659	-0.338	1.3182	0.0631	0.0084	-0.1396	0.0116	0.0158	0.0757	0.097	-0.0663	-0.0842	0.083	-0.0103	-0.0244	0.0789	0.0053	0.1554	78.0522	33.8075	47.8125
5	0.5167	0.1105	-0.1847	1.3837	-0.523	1.3182	0.0275	-0.0204	-0.0027	0.0019	0.0195	0.0669	0.0505	0.0515	-0.0508	0.0758	-0.0021	-0.0106	0.1024	0.0031	0.1328	79.201	31.0636	55.1101
6	1.8763	-0.5915	0.1603	2.2602	-0.8463	2.2072	-0.0992	0.0831	-0.141	0.0008	0.0754	0.2404	0.0292	-0.1515	-0.0302	0.114	-0.0075	-0.0031	0.134	-0.002	0.2165	87.1396	19.7597	20.5157
7	0.5736	0.1247	-0.1626	0.7925	-0.0894	0.8339	-0.0031	0.085	-0.0321	-0.0461	0.0529	0.1116	-0.0521	-0.0718	-0.0026	0.1178	0.0105	-0.0316	0.1107	-0	0.1362	93.0831	26.6229	15.8778
8	1.4974	-0.0028	0.2041	0.9409	-0.2459	0.8507	0.0253	0.1703	-0.113	-0.2763	-0.0619	-0.0558	0.185	0.0735	-0.008	0.1625	0.0235	-0.01	0.1422	-0.0139	0.159	98.0523	21.0143	12.7716
9	0.6407	-0.028	-0.0616	1.7483	-0.3539	1.2858	-0.0164	-0.0033	-0.1939	-0.0041	0.0703	0.2051	0.013	-0.027	0.0201	0.1125	0.0074	0.0018	0.1062	-0	0.1634	94.962	22.2362	22.4914
10	1.2397	-0.1577	-0.0424	2.0178	-0.9793	1.7846	-0.0197	0.1685	-0.0281	-0.1293	0.0311	0.3116	-0.1561	-0.1549	-0.0931	0.1619	0.0195	-0.0443	0.1402	0.0035	0.1507	88.4675	29.1861	17.9356
11	3.3031	-2.5868	-2.1866	2.7285	1.6582	1.6235	-0.0297	0.0884	-0.0192	0.0231	-0.0723	0.0429	0.0259	-0.1021	0.1169	0.0915	-0.015	-0.0267	0.0995	-0.0034	0.1395	71.9657	26.7949	46.1307
12	4.9237	-2.5531	-0.5787	1.9276	-0.0924	0.4555	0.0887	0.2924	-0.1139	-0.1209	-0.1514	0.0773	0.046	-0.1638	0.0655	0.095	-0.0169	-0.0159	0.1548	-0.0239	0.1425	76.2778	21.7709	35.8372
13	3.4248	-0.3017	-0.3129	1.2544	0.2983	0.604	-0.0051	0.2015	0.1076	-0.0821	-0.0078	-0.0395	-0.0008	-0.1471	0.0233	0.0881	-0.0226	0.0001	0.1319	0.0056	0.0912	77.7713	26.5433	37.7907
14	2.7955	-0.167	-0.161	0.7574	0.306	0.8388	-0.0346	0.1589	0.0458	-0.097	-0.1138	0.2564	-0.0665	-0.2201	0.1041	0.1138	-0.0105	-0.0388	0.1662	-0.0184	0.1689	64.7284	29.2163	41.2685
15	7.6522	-4.7533	-6.1679	5.7772	4.9462	7.7029	-0.3698	0.2919	-0.5951	0.2446	-0.092	0.4718	0.2494	-0.3418	0.4399	0.1115	-0.0374	0.0004	0.1511	-0.0154	0.157	64.2637	21.8969	43.8612
16	1.4193	-0.1013	-0.203	5.844	-0.708	2.7344	0.009	-0.0601	-0.0437	-0.0423	-0.1007	-0.2098	-0.0679	0.0322	0.0906	0.0645	0.0198	-0.0004	0.0894	0.0023	0.1167	76.8706	47.3713	64.726
17	3.6265	0.6681	-0.0041	6.0766	1.0373	0.3427	0.1584	0.1212	0.0512	0.0203	-0.3043	-0.5159	-0.1399	-0.0239	0.1551	0.1333	-0.0125	0.0126	0.1016	0.0069	0.0892	79.6185	51.6944	61.6187
18	2.8535	2.526	2.0706	2.91	2.913	3.3945	-0.0175	0.0038	0.207	-0.2184	-0.1729	0.2874	-0.2244	-0.1042	0.2034	0.1353	0.0071	-0.0117	0.1021	0.0058	0.1576	71.7396	51.5515	58.9329
19	1.0316	0.2804	0.4109	2.2317	2.0614	3.0959	-0.0613	0.0004	0.1267	0.0472	-0.1543	0.2553	-0.0248	-0.1989	0.2211	0.1072	0.0108	-0.0072	0.1237	-0.01	0.1682	69.5456	48.952	67.2839
20	1.6442	2.727	2.676	6.5755	2.9796	5.4854	0.0067	-0.0783	0.083	0.1306	-0.058	0.1232	-0.0665	-0.1461	0.0448	0.07	0.0243	-0.0153	0.0822	0.0045	0.1377	74.1472	49.3079	69.8632

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 2 through 75 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 76 through 87 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 88 through 106 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 107 through 134 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 135 through 216 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 2 through 18 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 19 through 48 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 49 through 75 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 76 through 91 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 92 through 106A)
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 107 through 137 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 138 through 150 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 151 through 173 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 174 through 197 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 198 through 212 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 0 through 12 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 13 through 22 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 23 through 37 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 38 through 46 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 47 through 57 )

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