PDB-8jza: Crystal structure of single domain antibody kt75 of human Thyrogl...

ID or keywords:

Entry

Database: PDB / ID: 8jza

Title

Crystal structure of single domain antibody kt75 of human Thyroglobulin

Components

single domain antibody kt75 of human Thyroglobulin

Keywords

IMMUNE SYSTEM / single domain antibodies Thyroglobulin nanobodies

Function / homology

ACETATE ION / :

Function and homology information

Biological species

Camelus dromedarius (Arabian camel)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Mistry, H. / Kumarasamy, J. / Kumari, S. / Kulkarni, S.P. / Gupta, G.D.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal structure of single domain antibody kt75 of human Thyroglobulin
Authors: Mistry, H. / Kumarasamy, J. / Kumari, S. / Kulkarni, S.P. / Gupta, G.D.

History

Deposition	Jul 4, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8jza.cif.gz	104.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8jza.ent.gz	77.8 KB	Display	PDB format
PDBx/mmJSON format	8jza.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jz/8jza ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jza	HTTPS FTP

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Related structure data

Similar structure data	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

A: single domain antibody kt75 of human Thyroglobulin

hetero molecules

15.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, monomer

Unit cell

Length a, b, c (Å)	38.751, 47.589, 64.237
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	single domain antibody kt75 of human Thyroglobulin Mass: 14837.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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 Å³/Da / Density % sol: 38.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4M K-acetate, 0.1 M sodium HEPES pH 7.0, 10% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97777 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97777 Å / Relative weight: 1
Reflection	Resolution: 1.35→38.75 Å / Num. obs: 26851 / % possible obs: 100 % / Redundancy: 7.9 % / B_iso Wilson estimate: 12.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.021 / R_rim(I) all: 0.059 / Χ²: 0.98 / Net I/σ(I): 18
Reflection shell	Resolution: 1.35→1.37 Å / Redundancy: 7.8 % / R_merge(I) obs: 0.916 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1329 / CC_1/2: 0.764 / R_pim(I) all: 0.349 / R_rim(I) all: 0.981 / Χ²: 1.01 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PHENIX	1.19.1	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.35→38.239 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.972 / SU B: 1.824 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.05

	R_factor	Num. reflection	% reflection
R_free	0.1744	1319	4.922 %
R_work	0.1304	25477	-
all	0.133	-	-
obs	-	26796	99.989 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 22.737 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.881 Å²	0 Å²	-0 Å²
2-	-	-0.44 Å²	0 Å²
3-	-	-	-0.441 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→38.239 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	978	0	13	93	1084

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	1054
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	888
X-RAY DIFFRACTION	r_angle_refined_deg	1.621	1.639	1434
X-RAY DIFFRACTION	r_angle_other_deg	0.577	1.569	2015
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.795	5	138
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.852	22	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.769	15	164
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.117	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	130
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	1223
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	247
X-RAY DIFFRACTION	r_nbd_refined	0.386	0.2	177
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	847
X-RAY DIFFRACTION	r_nbtor_refined	0.2	0.2	492
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	576
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	56
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.431	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.31	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	4.907	2.104	528
X-RAY DIFFRACTION	r_mcbond_other	4.72	2.069	520
X-RAY DIFFRACTION	r_mcangle_it	5.175	3.133	660
X-RAY DIFFRACTION	r_mcangle_other	5.104	3.109	657
X-RAY DIFFRACTION	r_scbond_it	5.148	2.365	526
X-RAY DIFFRACTION	r_scbond_other	5.143	2.364	527
X-RAY DIFFRACTION	r_scangle_it	6.079	3.412	770
X-RAY DIFFRACTION	r_scangle_other	6.075	3.411	771
X-RAY DIFFRACTION	r_lrange_it	5.598	38.822	4463
X-RAY DIFFRACTION	r_lrange_other	5.486	38.42	4387
X-RAY DIFFRACTION	r_rigid_bond_restr	9.416	3	1942

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.35-1.385	0.27	103	0.217	1871	0.22	1974	0.885	0.913	100	0.188
1.385-1.423	0.225	94	0.186	1791	0.188	1885	0.921	0.932	100	0.16
1.423-1.464	0.208	90	0.166	1755	0.168	1845	0.932	0.944	100	0.137
1.464-1.509	0.201	83	0.141	1711	0.144	1794	0.962	0.96	100	0.113
1.509-1.559	0.165	77	0.119	1676	0.121	1753	0.97	0.972	100	0.094
1.559-1.613	0.152	91	0.103	1597	0.106	1688	0.973	0.977	100	0.082
1.613-1.674	0.197	88	0.102	1525	0.107	1613	0.956	0.977	100	0.082
1.674-1.742	0.159	80	0.1	1513	0.103	1593	0.968	0.98	100	0.083
1.742-1.819	0.144	66	0.098	1438	0.1	1504	0.974	0.983	100	0.085
1.819-1.908	0.182	56	0.105	1384	0.108	1440	0.963	0.979	100	0.094
1.908-2.011	0.161	72	0.105	1314	0.108	1386	0.97	0.983	100	0.097
2.011-2.133	0.164	71	0.103	1237	0.105	1308	0.965	0.982	100	0.097
2.133-2.279	0.167	59	0.108	1195	0.111	1255	0.967	0.98	99.9203	0.106
2.279-2.461	0.176	57	0.114	1084	0.117	1141	0.967	0.979	100	0.115
2.461-2.695	0.174	54	0.13	1012	0.133	1066	0.967	0.975	100	0.134
2.695-3.011	0.168	59	0.138	920	0.14	979	0.972	0.974	100	0.145
3.011-3.473	0.136	38	0.127	826	0.127	864	0.978	0.98	100	0.144
3.473-4.245	0.146	34	0.133	715	0.134	749	0.981	0.98	100	0.159
4.245-5.967	0.184	29	0.149	565	0.151	594	0.968	0.977	100	0.183
5.967-38.239	0.307	18	0.25	348	0.253	368	0.929	0.935	99.4565	0.309

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