PDB-3dgg: Crystal structure of FabOX108

ID or keywords:

Entry

Database: PDB / ID: 3dgg

Title

Crystal structure of FabOX108

Components

FabOX108 Heavy Chain Fragment
FabOX108 Light Chain Fragment

Keywords

IMMUNE SYSTEM / Antibody fragments / Fabs / Transient expression / Structural Genomics / Oxford Protein Production Facility / OPPF / Immunoglobulin domain

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: 2.3 Å

Authors

Ren, J. / Nettleship, J.E. / Owens, R.J. / Oxford Protein Production Facility (OPPF)

Citation

Journal: Protein Expr.Purif. / Year: 2008
Title: A pipeline for the production of antibody fragments for structural studies using transient expression in HEK 293T cells.
Authors: Nettleship, J.E. / Ren, J. / Rahman, N. / Berrow, N.S. / Hatherley, D. / Barclay, A.N. / Owens, R.J.

History

Deposition	Jun 13, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Mar 31, 2021	Group: Database references / Derived calculations / Source and taxonomy Category: entity_src_gen / struct_ref_seq_dif / struct_site Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 30, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5	Oct 16, 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	3dgg.cif.gz	185.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dg/3dgg ftp://data.pdbj.org/pub/pdb/validation_reports/dg/3dgg	HTTPS FTP

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Related structure data

Related structure data	3difC 32c2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ck0-d 3okm-d 6med-1 5ijk-1 5mv3-7 5bk3-2 5dyo-1 6ks2-2 5vzr-1 5mv3-8 3pho-d 7c95-1 4mhj-7 1bfo-4 4m61-2 1mrc-d 5mv3-3 2gsi-4 6tcp-1 5tdo-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

3difC

32c2S

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: FabOX108 Light Chain Fragment

B: FabOX108 Heavy Chain Fragment

C: FabOX108 Light Chain Fragment

D: FabOX108 Heavy Chain Fragment

hetero molecules

97.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: FabOX108 Light Chain Fragment

B: FabOX108 Heavy Chain Fragment

hetero molecules

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

2

C: FabOX108 Light Chain Fragment

D: FabOX108 Heavy Chain Fragment

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	78.225, 52.142, 112.123
Angle α, β, γ (deg.)	90.00, 103.14, 90.00
Int Tables number	3
Space group name H-M	P121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	GLN	GLN	A	A	3 - 93	3 - 93
2	1	1	VAL	VAL	GLN	GLN	C	C	3 - 93	3 - 93
3	2	1	LEU	LEU	LEU	LEU	A	A	99 - 107	99 - 107
4	2	1	LEU	LEU	LEU	LEU	C	C	99 - 107	99 - 107
1	1	2	ALA	ALA	LYS	LYS	A	A	112 - 210	112 - 210
2	1	2	ALA	ALA	LYS	LYS	C	C	112 - 210	112 - 210
1	1	3	VAL	VAL	ASN	ASN	B	B	2 - 61	2 - 61
2	1	3	VAL	VAL	ASN	ASN	D	D	2 - 61	2 - 61
3	2	3	LYS	LYS	THR	THR	B	B	67 - 116	67 - 116
4	2	3	LYS	LYS	THR	THR	D	D	67 - 116	67 - 116
1	1	4	THR	THR	ALA	ALA	B	B	122 - 131	122 - 131
2	1	4	THR	THR	ALA	ALA	D	D	122 - 131	122 - 131
3	2	4	SER	SER	SER	SER	B	B	140 - 191	140 - 191
4	2	4	SER	SER	SER	SER	D	D	140 - 191	140 - 191
5	3	4	VAL	VAL	ILE	ILE	B	B	199 - 216	199 - 216
6	3	4	VAL	VAL	ILE	ILE	D	D	199 - 216	199 - 216

NCS ensembles :

ID
1
2
3
4

#1: Antibody	FabOX108 Light Chain Fragment / VL Mass: 23854.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pOPING-ET / Cell line (production host): HEK293T / Organ (production host): Human embryonic kidney cells / Production host: Homo sapiens (human)
#2: Antibody	FabOX108 Heavy Chain Fragment / VH Mass: 24977.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pOPING-ET / Cell line (production host): HEK293T / Organ (production host): Human embryonic kidney cells / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE SEQUENCE OF ENTITIES 1 AND 2 WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCE OF ENTITIES 1 AND 2 WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2M Ammonium sulfate, 5% v/v Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. obs: 39870 / % possible obs: 98.1 % / Observed criterion σ(I): -1.5 / Redundancy: 5.3 % / R_merge(I) obs: 0.101 / Net I/σ(I): 16.3
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.649 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3322 / % possible all: 83.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345	CCD	data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 32C2

32c2

Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.912 / SU B: 14.973 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24615	1947	5 %	RANDOM
R_work	0.18736	-	-	-
obs	0.19027	37098	98.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 43.909 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.32 Å²	0 Å²	-0.82 Å²
2-	-	-0.18 Å²	0 Å²
3-	-	-	-1.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6603	0	6	367	6976

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	6779
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4517
X-RAY DIFFRACTION	r_angle_refined_deg	1.061	1.952	9238
X-RAY DIFFRACTION	r_angle_other_deg	0.766	3.003	11060
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.87	5	853
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.58	24.394	264
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.755	15	1085
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.29	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1030
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	7499
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1313
X-RAY DIFFRACTION	r_nbd_refined	0.175	0.2	1069
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	4416
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	3129
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	3577
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	274
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.14	0.2	34
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.17	0.2	78
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.143	0.2	18
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.352	4	5473
X-RAY DIFFRACTION	r_mcbond_other	0.839	4	1719
X-RAY DIFFRACTION	r_mcangle_it	4.297	6	6955
X-RAY DIFFRACTION	r_scbond_it	5.27	6	3022
X-RAY DIFFRACTION	r_scangle_it	7.107	10	2283
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	585	medium positional	0.16	0.5
2	A	585	medium positional	0.18	0.5
3	B	646	medium positional	0.17	0.5
4	B	468	medium positional	0.14	0.5
1	A	682	loose positional	0.63	5
2	A	698	loose positional	0.8	5
3	B	813	loose positional	0.64	5
4	B	500	loose positional	0.45	5
1	A	585	medium thermal	2.37	20
2	A	585	medium thermal	2.39	20
3	B	646	medium thermal	2.31	20
4	B	468	medium thermal	2.98	20
1	A	682	loose thermal	3.32	30
2	A	698	loose thermal	3.79	30
3	B	813	loose thermal	3.3	30
4	B	500	loose thermal	2.88	30

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.364	135	-
R_work	0.265	2345	-
obs	-	-	85.37 %

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	2.1519	-0.0587	2.3527	1.8484	-1.4099	5.77	0.1477	0.1627	-0.1395	0.1322	0.0599	0.0928	0.2444	0.1669	-0.2077	-0.1428	0.0264	0.0092	-0.1201	-0.0102	-0.1311	-34.0703	-34.0703	-13.5987
2	1.5952	0.919	1.5979	2.2118	1.9351	5.4393	0.2229	-0.1117	-0.1626	0.0822	-0.0763	-0.0085	0.3893	-0.1213	-0.1467	-0.1675	0.029	0.0072	-0.1526	-0.0097	-0.114	-18.5979	-18.5979	21.8864
3	1.1675	-0.1804	0.5741	2.5559	-0.1581	3.7428	-0.0925	0.0731	0.0722	0.0589	-0.1215	-0.2332	-0.1057	0.1657	0.2141	-0.1915	-0.0354	-0.0151	-0.1047	0.0438	-0.084	-26.369	-80.268	-12.426
4	3.5878	-0.7146	2.5101	7.3172	-2.3594	4.2688	-0.1472	0.3879	-0.1035	-0.2833	-0.1416	-0.7579	-0.0755	0.69	0.2888	-0.0718	-0.0392	0.128	0.0405	-0.0031	-0.1042	-9.507	-93.551	11.277
5	2.0804	0.0111	0.6639	2.2385	-1.0905	5.2178	-0.0521	-0.0082	0.0431	0.1136	-0.0118	0.0384	-0.1859	0.2911	0.0639	-0.2077	-0.0199	-0.0028	-0.062	-0.0241	-0.15	-37.533	-75.798	-41.215
6	10.0091	1.3155	6.781	2.0694	0.8095	7.1708	-0.3418	-0.9321	0.6497	0.0352	-0.1114	0.3333	-0.5876	-0.7946	0.4531	-0.0825	0.094	-0.0151	0.005	-0.067	0.0216	-58.268	-66.959	-70.196
7	4.9185	0.5688	0.4165	2.4059	-0.7231	3.0559	-0.3418	0.2209	-0.2533	-0.2086	0.2462	-0.1335	0.2119	-0.0036	0.0956	-0.1075	-0.0404	0.0579	-0.1188	-0.0367	-0.1688	-44.827	-96.685	-44.005
8	5.0567	1.7361	1.7259	4.7074	-0.4224	2.518	0.0366	0.2106	0.3156	-0.2663	-0.0344	0.1649	0.0795	0.0597	-0.0022	-0.2102	0.0267	0.0198	-0.0883	-0.0239	-0.1412	-50.869	-80.305	-75.744

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 112	1 - 112
2	X-RAY DIFFRACTION	2	A	A	113 - 217	113 - 217
3	X-RAY DIFFRACTION	3	B	B	1 - 112	1 - 112
4	X-RAY DIFFRACTION	4	B	B	113 - 219	113 - 219
5	X-RAY DIFFRACTION	5	C	C	1 - 112	1 - 112
6	X-RAY DIFFRACTION	6	C	C	113 - 215	113 - 215
7	X-RAY DIFFRACTION	7	D	D	1 - 112	1 - 112
8	X-RAY DIFFRACTION	8	D	D	113 - 220	113 - 220

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