PDB-4r96: Structure of a Llama Glama Fab 48A2 against human cMet

ID or keywords:

Entry

Database: PDB / ID: 4r96

Title

Structure of a Llama Glama Fab 48A2 against human cMet

Components

Llama glama Fab 48A2 against human cMet H chain
Llama glama Fab 48A2 against human cMet L chain

Keywords

IMMUNE SYSTEM / Immunoglobulin domains / cMet

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Llama Glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.31 Å

Authors

Klarenbeek, A. / El Mazouari, K. / Desmyter, A. / Blanchetot, C. / Hultberg, A. / Roovers, R.C. / Cambillau, C. / Spinelli, S. / Del-Favero, J. / Verrips, T. ...

Citation

Journal: MAbs / Year: 2015
Title: Camelid Ig V genes reveal significant human homology not seen in therapeutic target genes, providing for a powerful therapeutic antibody platform.
Authors: Klarenbeek, A. / Mazouari, K.E. / Desmyter, A. / Blanchetot, C. / Hultberg, A. / de Jonge, N. / Roovers, R.C. / Cambillau, C. / Spinelli, S. / Del-Favero, J. / Verrips, T. / de Haard, H.J. / Achour, I.

History

Deposition	Sep 3, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 15, 2015	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 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	4r96.cif.gz	638.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4r96_validation.pdf.gz	491.5 KB	Display	wwPDB validaton report
Full document	4r96_full_validation.pdf.gz	533.1 KB	Display
Data in XML	4r96_validation.xml.gz	63.9 KB	Display
Data in CIF	4r96_validation.cif.gz	87.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r9/4r96 ftp://data.pdbj.org/pub/pdb/validation_reports/r9/4r96	HTTPS FTP

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Related structure data

Related structure data	4r90C 2vxsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ell-2 5b6f-2 5ijk-2 3inu-1 4zyk-2 5ik3-1 3mnv-2 5mv3-3 4mhj-9 6tcp-2 5mub-2 1aif-2 6be3-d 1clz-2 6cdm-1 5dlm-2 5vh4-1 5mv4-4 2vl5-2 5mv3-2 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

4r90C

2vxsS

S: Starting model for refinement

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

A: Llama glama Fab 48A2 against human cMet L chain

C: Llama glama Fab 48A2 against human cMet L chain

E: Llama glama Fab 48A2 against human cMet L chain

L: Llama glama Fab 48A2 against human cMet L chain

B: Llama glama Fab 48A2 against human cMet H chain

D: Llama glama Fab 48A2 against human cMet H chain

F: Llama glama Fab 48A2 against human cMet H chain

H: Llama glama Fab 48A2 against human cMet H chain

192 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Llama glama Fab 48A2 against human cMet L chain

B: Llama glama Fab 48A2 against human cMet H chain

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

2

C: Llama glama Fab 48A2 against human cMet L chain

D: Llama glama Fab 48A2 against human cMet H chain

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

3

E: Llama glama Fab 48A2 against human cMet L chain

F: Llama glama Fab 48A2 against human cMet H chain

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

4

L: Llama glama Fab 48A2 against human cMet L chain

H: Llama glama Fab 48A2 against human cMet H chain

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

Unit cell

Length a, b, c (Å)	107.020, 121.540, 185.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Llama glama Fab 48A2 against human cMet L chain Mass: 24425.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Llama Glama (llama) / Cellular location (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Llama glama Fab 48A2 against human cMet H chain Mass: 23458.064 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Llama Glama (llama) / Cellular location (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.16 Å³/Da / Density % sol: 61.03 %
Crystal grow	Temperature: 277 K / pH: 6 Details: in 1.4 M Na Malonate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.931
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
Radiation	Monochromator: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 3.3→45 Å / Num. obs: 35909 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 34.94 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shell	Resolution: 3.3→3.4 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.586 / Mean I/σ(I) obs: 2.4 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
MOLREP		phasing
BUSTER	2.9.2	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VXS

2vxs

Resolution: 3.31→43.39 Å / Cor.coef. F_o:F_c: 0.802 / Cor.coef. F_o:F_c free: 0.741 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.261	3580	9.98 %	RANDOM
R_work	0.217	-	-	-
obs	0.221	35872	-	-
all	-	35872	-	-

Displacement parameters

B_iso mean: 44.43 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	21.2825 Å²	0 Å²	0 Å²
2-	-	-33.0381 Å²	0 Å²
3-	-	-	11.7556 Å²

Refine analyze

Luzzati coordinate error obs: 0.673 Å

Refinement step

Cycle: LAST / Resolution: 3.31→43.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13302	0	0	234	13536

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	13620	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.25	18546	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		4481	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		313	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1977	HARMONIC	5
X-RAY DIFFRACTION	t_it		13620	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.82
X-RAY DIFFRACTION	t_other_torsion	22.95
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion	0	1799	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	0	14395	SEMIHARMONIC	4

LS refinement shell

Resolution: 3.31→3.41 Å / Total num. of bins used: 18

	R_factor	Num. reflection	% reflection
R_free	0.3146	277	9.95 %
R_work	0.2392	2508	-
all	0.2468	2785	-

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	0.7899	-0.082	-0.8379	0.0547	-1.1017	1.0582	-0.0011	0.0005	0.0062	0.0022	-0.0006	-0.013	-0.0015	-0.0059	0.0017	-0.0368	0.052	0.0273	0.0407	0.0251	-0.0175	-4.5562	19.4123	5.6244
2	0.7466	-0.4912	0.0788	0	-0.4576	0.1743	0.0002	0.0058	-0.0038	-0.0025	0.0003	0.0021	0.0011	0.0006	-0.0005	-0.0297	-0.0127	0.0119	0.0208	0.0119	0.0108	28.2859	14.63	-13.9002
3	0.4721	-0.5534	-0.6322	0.4024	0.9015	0.4233	-0.0014	0.0074	-0.0097	0.0106	-0.0077	0.0067	0.0087	-0.0072	0.0091	0.0059	-0.0262	0.0282	0.0143	-0.0291	-0.0091	-13.2228	16.3945	-14.1089
4	0.7123	0.5093	-0.592	0.5765	-1.0471	0.2806	0.0021	0.0208	0.0017	0.0081	0.0033	-0.0045	0.0136	-0.0048	-0.0054	-0.0069	0.0264	-0.0202	0.0236	0.0151	0.0241	15.1544	6.2118	-20.095
5	0.6603	0.0345	0.1246	0	0.2979	0.9201	0.0021	0.0039	0.0031	-0.0094	0.0002	0.005	0.0018	-0.0015	-0.0023	-0.022	-0.0001	0.0032	0.0451	0.0007	-0.0094	42.8072	-21.6385	-27.4661
6	1.1688	0.1944	0.4261	0	0.7966	0.2753	0.0012	0.0144	0.0081	-0.0013	0.0079	0.0157	-0.0036	-0.0014	-0.0092	-0.0286	0.0034	-0.0154	0.032	-0.0191	0.0059	9.8926	-15.9539	-6.0619
7	0.3571	0.0013	-0.0208	0.0347	0.3959	0.5049	-0.0011	-0.0115	0.0033	-0.0073	-0.003	-0.0084	0.0025	-0.001	0.0041	-0.0129	0.0102	-0.021	0.021	0.0088	0.0073	50.9494	-12.2091	-9.7127
8	0.6091	-0.329	-0.3626	0.2041	-0.5075	0.6765	0.0002	-0.0008	-0.0091	0.0029	-0.0031	-0.0008	-0.0015	-0.0007	0.0029	-0.0054	-0.0244	0.0018	0.0299	0.019	0.0025	24.711	-18.1405	2.7326
9	0.3709	0.3622	0.0707	0.0001	1.0296	0.947	0.0021	0.0115	-0.0063	-0.0071	0.0032	0.0159	-0.008	0.0051	-0.0053	-0.0221	-0.0262	-0.0042	0.0398	-0.0087	-0.0151	63.9028	18.3713	6.1062
10	1.0816	0.6079	0.6661	0	0.8953	0.5083	0.003	0.0056	0.0101	0.0008	-0.0047	0.0114	-0.0034	0.0006	0.0018	-0.0178	0.0106	0.051	0.0338	-0.0407	-0.0081	31.5928	18.2786	24.7358
11	0.4784	-0.1377	0.2621	0.252	0.1107	0.7108	0.002	-0.0026	-0.0084	-0.0049	-0.0065	-0.0054	0.0089	0.0049	0.0045	0.0009	0.042	0.0071	0.0207	-0.0103	-0.002	72.4376	19.0122	26.0479
12	0.3275	0.0132	-0.3385	0.2942	-0.0901	1.4466	0	-0.0004	-0.0068	0.0039	0.0055	0.0003	-0.0074	-0.0042	-0.0055	0.0269	-0.022	-0.0038	0.0123	-0.0081	-0.0055	43.3844	9.8749	33.9655
13	1.0488	-0.281	0.3802	0.2035	0.5607	0.9435	0.0003	-0.0037	-0.0005	0.0077	0.0006	-0.0063	0.0084	-0.0035	-0.0009	-0.0184	-0.0062	-0.0028	0.0343	0.0077	-0.002	27.7531	-35.152	25.4142
14	0.9704	0.2311	-0.8118	0	0.8044	0.1691	-0.0009	-0.0056	-0.0064	0.0107	-0.0045	-0.0052	0.0004	-0.0019	0.0054	-0.0296	-0.0109	0.0084	0.028	-0.0029	-0.0079	61.3956	-25.5282	39.6278
15	0.4292	0.061	-0.0646	0.1258	0.4839	0.5933	0	-0.0036	0.0046	-0.0024	0.0054	0.0137	-0.0035	0.0034	-0.0054	-0.0039	0.0053	-0.0233	0.0306	-0.0076	-0.0331	20.7651	-22.7313	41.7955
16	0.0174	0.0309	-0.0099	0.1228	0.0158	0.0116	0	-0.0009	0	-0.0016	-0.0007	-0.0007	0	0.0004	0.0007	0.0064	-0.0001	-0.0067	0.006	0.0011	0.002	33.2938	-17.578	46.2474

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{L\|0 - L\|110}
2	X-RAY DIFFRACTION	2	{L\|111 - L\|220}
3	X-RAY DIFFRACTION	3	{H\|1 - H\|110}
4	X-RAY DIFFRACTION	4	{H\|111 - H\|219}
5	X-RAY DIFFRACTION	5	{A\|0 - A\|110}
6	X-RAY DIFFRACTION	6	{A\|111 - A\|218}
7	X-RAY DIFFRACTION	7	{B\|1 - B\|110}
8	X-RAY DIFFRACTION	8	{B\|111 - B\|219}
9	X-RAY DIFFRACTION	9	{C\|0 - C\|110}
10	X-RAY DIFFRACTION	10	{C\|111 - C\|218}
11	X-RAY DIFFRACTION	11	{D\|1 - D\|110}
12	X-RAY DIFFRACTION	12	{D\|111 - D\|219}
13	X-RAY DIFFRACTION	13	{E\|0 - E\|110}
14	X-RAY DIFFRACTION	14	{E\|111 - E\|220}
15	X-RAY DIFFRACTION	15	{F\|1 - F\|110}
16	X-RAY DIFFRACTION	16	{F\|111 - F\|119}

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