PDB-5ibt: UCA Fab (unbound) from 6515 Lineage

ID or keywords:

Entry

Database: PDB / ID: 5ibt

Title

UCA Fab (unbound) from 6515 Lineage

Components

UCA Heavy Chain
UCA Light Chain

Keywords

IMMUNE SYSTEM / antibody / influenza / unbound

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: 2.4 Å

Authors

Raymond, D.D. / Harrison, S.C.

Funding support

United States, 1items

Citation

Journal: Nat. Med. / Year: 2016
Title: Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain.
Authors: Raymond, D.D. / Stewart, S.M. / Lee, J. / Ferdman, J. / Bajic, G. / Do, K.T. / Ernandes, M.J. / Suphaphiphat, P. / Settembre, E.C. / Dormitzer, P.R. / Del Giudice, G. / Finco, O. / Kang, T.H. ...

History

Deposition	Feb 22, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references
Revision 1.2	Dec 14, 2016	Group: Database references
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 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	5ibt.cif.gz	183.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ibt.ent.gz	146.8 KB	Display	PDB format
PDBx/mmJSON format	5ibt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ibt_validation.pdf.gz	447.6 KB	Display	wwPDB validaton report
Full document	5ibt_full_validation.pdf.gz	449 KB	Display
Data in XML	5ibt_validation.xml.gz	17.6 KB	Display
Data in CIF	5ibt_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/5ibt ftp://data.pdbj.org/pub/pdb/validation_reports/ib/5ibt	HTTPS FTP

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Related structure data

Related structure data	5iblC 5ibuSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4wy7-d 4xcn-2 2v17-d 6wfz-1 3qct-d 6obd-2 2y6s-1 4m93-1 5mhg-d 6lun-2 5mv3-6 6x1s-4 6o3u-2 5it2-d 3sgd-1 6ute-3 1mnu-d 6ldy-2 2a6i-d 2a77-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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: UCA Heavy Chain

L: UCA Light Chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	51.840, 63.390, 146.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	UCA Heavy Chain Mass: 24626.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	UCA Light Chain Mass: 23446.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.5 Å³/Da / Density % sol: 50.84 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.5 M NaCl, 0.05 M Tris-HCL pH 8.5, 22% PEG 4000 and 20% glycerol as a cryoprotectant

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Data collection

Diffraction

Mean temperature: 173.15 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.99996 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.99996 Å / Relative weight: 1

Reflection

Resolution: 2.4→48.87 Å / Num. obs: 19340 / % possible obs: 98.8 % / Redundancy: 7.1 % / B_iso Wilson estimate: 56.45 Å² / R_merge(I) obs: 0.2 / Net I/σ(I): 10.7

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.4-2.55	2.366	1.06	1	94.6
2.55-2.72	1.469	1.87	1	99.5
2.72-2.94	0.805	3.24	1	99.5
2.94-3.22	0.38	6.26	1	99.7
3.22-3.6	0.169	12.13	1	99.7
3.6-4.15	0.096	18.69	1	99.8
4.15-5.08	0.059	27.19	1	99.9
5.08-7.14	0.073	23.19	1	99.9
7.14-48.87	0.036	36.8	1	99.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.2	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IBU

5ibu

Resolution: 2.4→48.87 Å / Cor.coef. F_o:F_c: 0.9337 / Cor.coef. F_o:F_c free: 0.8864 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.397 / SU R_free Blow DPI: 0.28 / SU R_free Cruickshank DPI: 0.28

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2775	967	5 %	RANDOM
R_work	0.2049	-	-	-
obs	0.2085	19340	98.85 %	-

Displacement parameters

B_iso mean: 50.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.8857 Å²	0 Å²	0 Å²
2-	-	3.944 Å²	0 Å²
3-	-	-	-2.0583 Å²

Refine analyze

Luzzati coordinate error obs: 0.378 Å

Refinement step

Cycle: LAST / Resolution: 2.4→48.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3308	0	12	89	3409

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	3404	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.26	4630	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1118	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		68	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		496	HARMONIC	5
X-RAY DIFFRACTION	t_it		3404	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.45
X-RAY DIFFRACTION	t_other_torsion	20.37
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		444	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3660	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.4→2.53 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.2873	131	4.98 %
R_work	0.2315	2497	-
all	0.2342	2628	-
obs	-	-	98.85 %

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	-2.6904	1.8082	0	-2.6472	0.04	-0.031	0.0277	0.4368	0.1743	-0.1272	0.0308	-0.2873	0.0602	0.1582	0.1411	0.0303	0.0065	-0.314	-0.0191	-0.0166	-21.1124	-14.1316	42.9445
2	0.495	-1.1382	-1.0968	1.1962	-3.5714	3.2577	0.0475	0.2601	-0.1698	0.0952	-0.0397	-0.2438	-0.3055	-0.0128	-0.0079	-0.0669	0.0481	-0.0476	-0.3337	-0.0471	0.0922	-24.33	-17.5367	37.7439
3	4.1958	-2.178	1.4973	4.7759	-0.5948	1.7538	0.0292	0.2828	0.0187	-0.0149	-0.2375	0.0103	-0.0535	0.0836	0.2083	0.0217	-0.0239	0.0136	-0.2241	-0.0063	0.0242	-15.1203	-19.3516	31.7301
4	0.2184	-1.5747	0.8568	1.6267	-0.1269	0.7079	-0.0165	0.3159	-0.1362	-0.2675	-0.0037	0.0421	0.0844	-0.0611	0.0202	0.1224	-0.009	-0.047	-0.1752	-0.0265	0.241	-21.8804	-21.5107	30.3449
5	0.9562	-0.0933	-0.0844	0.2697	-0.0626	0.4067	0.0481	-0.0001	0.0412	0.0795	0.0816	0.0364	-0.0772	-0.0275	-0.1297	0.0134	-0.0135	-0.0531	-0.2338	-0.036	0.0617	-15.0106	-21.0799	44.7634
6	1.5893	-1.1591	-1.3886	2.4762	-0.4169	2.6953	-0.1292	-0.668	0.2077	0.0229	0.0897	-0.0025	-0.6524	-0.0232	0.0395	0.0232	-0.0214	0.002	-0.2422	-0.0563	-0.0485	-12.5178	-24.3327	67.274
7	0	-3.2979	-4.0907	0	0.3755	4.3397	0.2069	-0.6164	0.6431	0.0441	0.0787	0.1264	-0.3589	0.2436	-0.2856	0.4153	0.1851	0.0764	-0.1161	-0.0765	0.0779	-18.1607	-19.5026	71.0512
8	2.7944	-3.601	-3.6715	4.7415	1.8433	0	0.0408	-0.0852	0.2485	0.2157	0.1726	0.1747	-0.2007	-0.1863	-0.2133	0.1833	0.025	0.0774	-0.1361	0.0088	-0.058	-20.5777	-23.0744	74.3417
9	4.032	-0.0838	-1.5606	0	-0.5642	0.6115	0.0947	-0.1712	0.0235	-0.2903	-0.4136	-0.2907	-0.1799	0.7826	0.3189	0.1043	-0.0008	-0.1282	-0.2235	0.0901	0.0645	6.9046	-22.7263	41.7063
10	0	-1.3573	-3.2605	0.8358	0.0959	1.4825	0.0641	0.1121	-0.0795	0.1529	-0.0943	0.117	-0.2029	0.3024	0.0302	-0.0825	0.0839	-0.038	-0.0881	0.0063	0.2007	9.6693	-20.3555	37.4123
11	6.4397	-2.7623	-0.3047	2.4811	-0.312	2.1035	0.0263	0.2045	-0.16	0.0496	-0.3139	-0.1135	-0.2276	0.4763	0.2876	-0.0732	-0.0615	-0.0472	-0.253	0.0067	0.029	-1.42	-17.1815	35.294
12	4.5065	-0.2052	3.9314	1.8563	-1.7809	8.417	-0.1114	0.4729	0.1938	0.0922	-0.2513	-0.3579	-0.7996	0.8457	0.3628	-0.0763	-0.0992	-0.0282	-0.1131	0.0675	-0.0055	3.3263	-15.0635	38.1257
13	3.9826	-0.9772	-0.9644	1.5404	-0.5898	1.9886	-0.1887	-0.9511	-0.0384	0.0286	0.2217	0.2656	0.0038	0.2746	-0.033	0.0028	-0.0128	-0.0622	-0.196	0.0224	-0.0999	-2.8686	-32.206	68.367
14	3.8278	-2.0353	-0.1625	0	1.7249	0	0.0374	-0.3136	-0.4551	-0.2496	0.0827	-0.4757	0.0964	0.224	-0.1201	0.0713	0.0348	-0.0359	-0.2456	-0.0386	0.0519	-4.2533	-43.4725	65.4488
15	0.1355	-2.679	0.7593	0.5141	1.621	1.5566	-0.058	-0.2997	-0.076	0.3417	0.195	-0.0341	-0.216	0.0911	-0.137	0.1698	0.0187	-0.1308	-0.2138	0.0682	-0.058	-5.0098	-31.2006	65.4323
16	0.9624	-0.8404	-2.141	3.9585	-4.117	4.5157	0.0247	-0.7916	-0.3995	0.447	-0.0058	-0.0816	-0.1301	0.182	-0.0189	0.172	0.0312	-0.0336	-0.074	0.1518	0.0185	0.8257	-40.5121	73.2272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{H\|1 - 12}
2	X-RAY DIFFRACTION	2	{H\|13 - 29}
3	X-RAY DIFFRACTION	3	{H\|30 - 58}
4	X-RAY DIFFRACTION	4	{H\|59 - 82}
5	X-RAY DIFFRACTION	5	{H\|83 - 151}
6	X-RAY DIFFRACTION	6	{H\|152 - 203}
7	X-RAY DIFFRACTION	7	{H\|204 - 214}
8	X-RAY DIFFRACTION	8	{H\|215 - 225}
9	X-RAY DIFFRACTION	9	{L\|1 - 17}
10	X-RAY DIFFRACTION	10	{L\|18 - 25}
11	X-RAY DIFFRACTION	11	{L\|26 - 46}
12	X-RAY DIFFRACTION	12	{L\|47 - 108}
13	X-RAY DIFFRACTION	13	{L\|109 - 148}
14	X-RAY DIFFRACTION	14	{L\|149 - 163}
15	X-RAY DIFFRACTION	15	{L\|164 - 188}
16	X-RAY DIFFRACTION	16	{L\|189 - 215}

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