PDB-6pzg: Crystal structure of human NA-80 Fab

ID or keywords:

Entry

Database: PDB / ID: 6pzg

Title

Crystal structure of human NA-80 Fab

Components

NA-80 Fab heavy chain
NA-80 Fab light chain

Keywords

IMMUNE SYSTEM /

antibody / inhibition mechanism

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Zhu, X. / Wilson, I.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	U19 AI117905	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201400024C	United States

Validation Report

Summary

Full report

About validation report

History

Deposition	Jul 31, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmcif format	6pzg.cif.gz / Display in browser / Tree view / PDBx/mmCIF dictionary
PDB format	pdb6pzg.ent.gz / Display in browser / PDB Contents Guide
PDBML Plus	6pzg-add.xml.gz / Display in browser / *PLUS
Others	Other downloads

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Related structure data

Related structure data	20538C 20540C 20541C 20594C 6pzdC 6pzeC 6pzfC 6pzhC 6pzwC 6pzyC 6pzzC 6u02C 4kmtS 5azeS S: Starting model for refinement C: citing same article (ref.)
Similar-shape strucutres	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)

Deposited unit

L: NA-80 Fab light chain

H: NA-80 Fab heavy chain

48.1 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
Download structure data

Unit cell

γ

α

β

Length a, b, c (Å)	102.770, 102.770, 80.359
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	L-534- HOH
2	1	H-365- HOH

#1: Antibody	NA-80 Fab light chain Mass: 23344.785 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	NA-80 Fab heavy chain Mass: 24793.639 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.: 446 / 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: 2.54 Å³/Da / Density % sol: 51.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M sodium citrate, pH 5.6, 40% PEG600

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.59→44.5 Å / Num. obs: 66498 / % possible obs: 99.9 % / Redundancy: 18.1 % / CC_1/2: 0.999 / R_pim(I) all: 0.02 / R_sym value: 0.08 / Net I/σ(I): 58
Reflection shell	Resolution: 1.59→1.62 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3234 / CC_1/2: 0.63 / R_pim(I) all: 0.35 / R_sym value: 0.9 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4kmt, 5aze

4kmt

5aze

Resolution: 1.59→44.5 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.78

	R_factor	Num. reflection	% reflection
R_free	0.2036	3374	5.08 %
R_work	0.1684	-	-
Obs	0.1702	66460	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.59→44.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3297	0	0	446	3743

Refine LS restraints

Refinement-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3468
X-RAY DIFFRACTION	f_angle_d	1.061	4754
X-RAY DIFFRACTION	f_dihedral_angle_d	11.174	2111
X-RAY DIFFRACTION	f_chiral_restr	0.063	539
X-RAY DIFFRACTION	f_plane_restr	0.007	611

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refinement-ID	% reflection obs (%)
1.5856-1.6083	0.3272	124	0.2777	2547	X-RAY DIFFRACTION	96
1.6083-1.6323	0.2929	127	0.2444	2596	X-RAY DIFFRACTION	100
1.6323-1.6578	0.2535	148	0.2268	2596	X-RAY DIFFRACTION	100
1.6578-1.685	0.2522	149	0.2129	2593	X-RAY DIFFRACTION	100
1.685-1.714	0.2525	160	0.2047	2620	X-RAY DIFFRACTION	100
1.714-1.7452	0.2181	136	0.1971	2592	X-RAY DIFFRACTION	100
1.7452-1.7787	0.2034	117	0.2002	2614	X-RAY DIFFRACTION	100
1.7787-1.8151	0.2479	148	0.1979	2604	X-RAY DIFFRACTION	100
1.8151-1.8545	0.2121	145	0.1998	2610	X-RAY DIFFRACTION	100
1.8545-1.8977	0.2186	134	0.1965	2623	X-RAY DIFFRACTION	100
1.8977-1.9451	0.2183	153	0.1879	2608	X-RAY DIFFRACTION	100
1.9451-1.9977	0.2316	157	0.1828	2596	X-RAY DIFFRACTION	100
1.9977-2.0565	0.2191	140	0.1812	2631	X-RAY DIFFRACTION	100
2.0565-2.1229	0.2361	144	0.1801	2610	X-RAY DIFFRACTION	100
2.1229-2.1987	0.198	134	0.1751	2615	X-RAY DIFFRACTION	100
2.1987-2.2868	0.209	120	0.1736	2682	X-RAY DIFFRACTION	100
2.2868-2.3908	0.1882	144	0.1727	2595	X-RAY DIFFRACTION	100
2.3908-2.5169	0.2044	147	0.1758	2650	X-RAY DIFFRACTION	100
2.5169-2.6746	0.1948	153	0.1682	2627	X-RAY DIFFRACTION	100
2.6746-2.881	0.2067	149	0.1703	2628	X-RAY DIFFRACTION	100
2.881-3.1709	0.1989	144	0.1734	2650	X-RAY DIFFRACTION	100
3.1709-3.6295	0.231	118	0.1577	2722	X-RAY DIFFRACTION	100
3.6295-4.5721	0.1797	150	0.1324	2666	X-RAY DIFFRACTION	100
4.5721-44.5182	0.1698	133	0.1546	2811	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refinement-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	7.4926	5.5059	-7.1161	4.1233	-5.1316	7.0224	0.4466	-0.4706	0.6009	0.3191	-0.1363	0.2093	-0.3435	0.3381	-0.345	0.2232	-0.0141	-0.0039	0.2524	-0.0634	0.2534	37.0948	-20.6704	19.6321
2	4.847	0.7741	-1.7045	2.9249	-1.087	3.0878	-0.0247	-0.275	-0.213	0.0699	-0.0875	-0.2086	0.1535	0.2198	0.0881	0.1769	0.0328	-0.0177	0.1831	-0.0007	0.1831	36.576	-29.0324	16.4339
3	2.9023	3.743	-4.3114	4.9832	-5.7088	6.6313	-0.1623	-0.1699	-0.3941	-0.0993	-0.1875	-0.4373	0.1706	0.2713	0.3628	0.1638	-0.0063	-0.002	0.2246	-0.0291	0.2036	44.2669	-9.8454	7.224
4	3.2715	-0.1761	2.3385	2.2117	0.0313	3.1626	0.0236	0.3626	0.3228	-1.2687	0.1276	0.5817	0.2919	-0.3112	0.2103	0.4445	-0.1241	-0.2781	0.3163	0.1454	0.3307	23.754	5.4214	-9.929
5	7.1475	-4.2588	0.857	4.75	-1.0989	1.5456	-0.046	-0.0964	-0.1466	-0.0834	0.2085	0.2154	-0.0228	0.0004	-0.11	0.1537	-0.0563	-0.0025	0.1659	0.0293	0.1804	31.6917	1.1218	2.4252
6	4.5942	-2.6414	-0.1373	6.1399	0.6376	1.064	0.0155	-0.0097	-0.3923	-0.0543	-0.0018	0.2681	0.0048	-0.0099	-0.0423	0.1555	-0.0368	0.0094	0.1787	0.0308	0.1108	31.898	-3.1401	2.2664
7	5.6395	-0.9308	1.2956	4.8431	-0.5177	2.4805	-0.2624	-0.1357	0.3626	-0.235	0.2193	0.8518	-0.3201	-0.3	-0.0023	0.1877	0.0047	-0.052	0.2155	0.0381	0.3037	22.3927	8.6291	-0.7424
8	8.1169	-3.3442	3.6089	5.4775	-1.4309	4.1682	-0.5288	-0.037	0.8416	0.1256	0.1984	-0.3022	-0.5485	0.0035	0.1888	0.1698	-0.0485	0.002	0.1858	-0.0057	0.1864	34.874	9.4844	1.6265
9	8.2412	-5.5973	-0.639	4.5069	0.0409	3.9853	0.2059	0.6315	-0.3189	-0.2531	-0.2671	0.3025	0.044	0.2043	0.0856	0.1655	-0.0469	-0.0473	0.2018	-0.0166	0.2407	17.8489	-30.5575	-1.341
10	3.5697	-1.3027	0.3824	3.1733	-0.1707	1.4075	-0.0989	0.0902	-0.3121	0.2682	0.0104	0.2942	0.1573	-0.158	0.078	0.2003	0.0053	0.0395	0.1883	-0.0248	0.2109	18.3321	-36.978	8.7576
11	5.7983	-1.4735	1.7662	4.8605	-1.7575	2.3963	-0.1361	0.1837	0.1891	0.1954	0.0669	0.2464	-0.0725	-0.1465	0.169	0.1296	0.0062	0.0208	0.1709	-0.0304	0.1457	16.7723	-27.3659	6.6627
12	1.1294	0.4146	0.4024	1.6168	0.3929	0.1896	-0.1769	0.1486	0.0244	-0.1991	0.1456	0.0269	0.0406	0.0396	-0.0575	0.1628	-0.0157	0.0168	0.2725	-0.0089	0.1575	25.1759	-18.4099	-0.6433
13	4.7932	2.3304	0.0654	2.0633	-0.7881	0.501	-0.9754	1.1973	-0.4194	-0.9251	0.7552	-0.168	0.2195	-0.047	0.0532	0.4616	-0.238	0.0437	0.451	-0.1207	0.2136	27.5168	-6.8031	-13.3987

Refinement TLS group

ID	Refinement-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN L AND RESID 0:25 )	L	0 - 25
2	X-RAY DIFFRACTION	2	( CHAIN L AND RESID 26:101 )	L	26 - 101
3	X-RAY DIFFRACTION	3	( CHAIN L AND RESID 102:113 )	L	102 - 113
4	X-RAY DIFFRACTION	4	( CHAIN L AND RESID 114:128 )	L	114 - 128
5	X-RAY DIFFRACTION	5	( CHAIN L AND RESID 129:150 )	L	129 - 150
6	X-RAY DIFFRACTION	6	( CHAIN L AND RESID 151:174 )	L	151 - 174
7	X-RAY DIFFRACTION	7	( CHAIN L AND RESID 175:197 )	L	175 - 197
8	X-RAY DIFFRACTION	8	( CHAIN L AND RESID 198:213 )	L	198 - 213
9	X-RAY DIFFRACTION	9	( CHAIN H AND RESID 1:17 )	H	1 - 17
10	X-RAY DIFFRACTION	10	( CHAIN H AND RESID 18:82 )	H	18 - 82
11	X-RAY DIFFRACTION	11	( CHAIN H AND RESID 83:95 )	H	83 - 95
12	X-RAY DIFFRACTION	12	( CHAIN H AND RESID 96:136 )	H	96 - 136
13	X-RAY DIFFRACTION	13	( CHAIN H AND RESID 137:228 )	H	137 - 228

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