PDB-2gjz: Structure of Catalytic Elimination Antibody 13G5 from a crystal i...

ID or keywords:

Entry

Database: PDB / ID: 2gjz

Title

Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)

Components

Catalytic elimination antibody 13G5 heavy chain
Catalytic elimination antibody 13G5 light chain

Keywords

IMMUNE SYSTEM / immunoglobulin / catalytic antibody / elimination

Function / homology

Function and homology information

immunoglobulin complex / adaptive immune response / extracellular region / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Debler, E.W. / Wilson, I.A.

Citation

Journal: J.Am.Chem.Soc. / Year: 2007
Title: Bifunctional Catalysis of Proton Transfer at an Antibody Active Site.
Authors: Muller, R. / Debler, E.W. / Steinmann, M. / Seebeck, F.P. / Wilson, I.A. / Hilvert, D.

History

Deposition	Mar 31, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gj/2gjz ftp://data.pdbj.org/pub/pdb/validation_reports/gj/2gjz	HTTPS FTP

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Related structure data

Related structure data	2gk0C 1hinS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1t04-1 5hdb-4 5u4r-1 4hzl-1 5jop-1 6qnk-2 3rvu-d 6i1o-d 6qnk-1 5gux-1 3ra7-1 1gaf-d 3qct-d 3i9g-d 2fx8-1 1bog-d 4xcn-2 5xhf-2 6h0e-4 6obd-1 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) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2gk0C

1hinS

C: citing same article (ref.)

S: Starting model for refinement

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

L: Catalytic elimination antibody 13G5 light chain

H: Catalytic elimination antibody 13G5 heavy chain

A: Catalytic elimination antibody 13G5 light chain

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

1

L: Catalytic elimination antibody 13G5 light chain

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

2

A: Catalytic elimination antibody 13G5 light chain

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

3

L: Catalytic elimination antibody 13G5 light chain

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

A: Catalytic elimination antibody 13G5 light chain

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

4

L: Catalytic elimination antibody 13G5 light chain

hetero molecules

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

A: Catalytic elimination antibody 13G5 light chain

hetero molecules

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

5

L: Catalytic elimination antibody 13G5 light chain

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

A: Catalytic elimination antibody 13G5 light chain

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

6

L: Catalytic elimination antibody 13G5 light chain

hetero molecules

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

A: Catalytic elimination antibody 13G5 light chain

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

7

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

A: Catalytic elimination antibody 13G5 light chain

hetero molecules

L: Catalytic elimination antibody 13G5 light chain

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

8

L: Catalytic elimination antibody 13G5 light chain

hetero molecules

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

H: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

A: Catalytic elimination antibody 13G5 light chain

hetero molecules

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

9

A: Catalytic elimination antibody 13G5 light chain

hetero molecules

B: Catalytic elimination antibody 13G5 heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.209, 73.495, 130.475
Angle α, β, γ (deg.)	90.00, 96.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-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	LEU	LEU	GLN	GLN	L	A	2 - 27	2 - 27
2	1	LEU	LEU	GLN	GLN	A	C	2 - 27	2 - 27
1	2	GLY	GLY	ILE	ILE	L	A	29 - 48	34 - 53
2	2	GLY	GLY	ILE	ILE	A	C	29 - 48	34 - 53
1	3	GLY	GLY	GLU	GLU	L	A	101 - 105	106 - 110
2	3	GLY	GLY	GLU	GLU	A	C	101 - 105	106 - 110
1	4	ARG	ARG	ASN	ASN	L	A	108 - 212	113 - 217
2	4	ARG	ARG	ASN	ASN	A	C	108 - 212	113 - 217
1	5	GLN	GLN	TRP	TRP	H	B	1 - 96	1 - 99
2	5	GLN	GLN	TRP	TRP	B	D	1 - 96	1 - 99
1	6	TYR	TYR	VAL	VAL	H	B	100 - 111	103 - 119
2	6	TYR	TYR	VAL	VAL	B	D	100 - 111	103 - 119
1	7	ALA	ALA	PRO	PRO	H	B	114 - 126	122 - 134
2	7	ALA	ALA	PRO	PRO	B	D	114 - 126	122 - 134
1	8	SER	SER	PRO	PRO	H	B	137 - 227	143 - 220
2	8	SER	SER	PRO	PRO	B	D	137 - 227	143 - 220
1	9	LYS	LYS	GLN	GLN	L	A	50 - 90	55 - 95
2	9	LYS	LYS	GLN	GLN	A	C	50 - 90	55 - 95

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9

Details

This entry contains the crystallographic asymmetric unit which consists of 2 biological molecules: LH, and AB

#1: Antibody	Catalytic elimination antibody 13G5 light chain Mass: 23939.566 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q65ZC0*PLUS
#2: Antibody	Catalytic elimination antibody 13G5 heavy chain Mass: 23481.295 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H₂O
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: 2.52 Å³/Da / Density % sol: 51.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, 0.1M MES, 0.2M Zn(OAc)2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 2.65→40 Å / Num. all: 28609 / Num. obs: 27894 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_sym value: 0.07 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.65→2.71 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.8 / R_sym value: 0.76 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
ADSC		data collection
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1HIN

1hin

Resolution: 2.65→40 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.92 / SU B: 30.53 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2496	1238	4.8 %	RANDOM
R_work	0.21312	-	-	-
obs	0.21494	24442	92.95 %	-
all	-	26296	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 94.943 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.54 Å²	0 Å²	2.14 Å²
2-	-	0.35 Å²	0 Å²
3-	-	-	-4.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6668	0	11	27	6706

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6848
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.431	1.952	9346
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.163	5	872
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.942	24.419	258
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.431	15	1078
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.535	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1050
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5164
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	2610
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	4583
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	205
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.215	0.2	8
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.26	0.2	43
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.298	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.145	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.489	1.5	4438
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.878	2	7098
X-RAY DIFFRACTION	r_scbond_it	1.22	3	2772
X-RAY DIFFRACTION	r_scangle_it	1.871	4.5	2248
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	L	187	tight positional	0.05	0.05
2	L	166	tight positional	0.16	0.05
3	L	37	tight positional	0.06	0.05
4	L	823	tight positional	0.09	0.05
5	H	759	tight positional	0.09	0.05
6	H	108	tight positional	0.04	0.05
7	H	94	tight positional	0.05	0.05
8	H	584	tight positional	0.09	0.05
9	L	320	tight positional	0.04	0.05
1	L	187	tight thermal	0.1	0.5
2	L	166	tight thermal	0.13	0.5
3	L	37	tight thermal	0.12	0.5
4	L	823	tight thermal	0.17	0.5
5	H	759	tight thermal	0.07	0.5
6	H	108	tight thermal	0.08	0.5
7	H	94	tight thermal	0.11	0.5
8	H	584	tight thermal	0.13	0.5
9	L	320	tight thermal	0.09	0.5

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	62	-
R_work	0.365	1452	-
obs	-	-	75.7 %

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	11.1848	-4.6655	0.8968	8.1436	0.2949	7.2235	0.5756	-0.2566	0.3314	-1.32	-0.1221	-0.3225	-0.5764	-0.3164	-0.4535	-0.4517	-0.0807	0.0742	-0.5937	0.0437	-0.5401	20.4202	46.485	19.7912
2	5.3163	0.2227	3.9119	3.3987	1.7643	19.7509	-0.0505	0.385	0.2175	0.7746	-0.0132	0.2826	-1.0674	0.1094	0.0638	-0.3185	0.0261	0.0539	-0.6954	0.0275	-0.5875	14.2539	52.6811	56.0626
3	10.0603	-3.2028	2.2138	7.2922	2.1038	13.5986	0.1926	-0.6144	-0.1714	-0.5123	0.4436	-1.0608	1.0013	1.8016	-0.6362	-0.5558	0.0418	0.1297	-0.2393	-0.0474	-0.2042	36.0533	33.4018	27.323
4	10.5384	-2.375	-1.1353	7.5979	2.5016	14.046	-0.1809	0.2535	-0.3433	1.3974	-0.033	0.5361	2.0068	-0.0969	0.2139	0.0924	0.0234	0.0711	-0.7228	0.0379	-0.6817	16.0821	37.0133	56.3141
5	10.2443	0.4155	-2.473	5.8515	-1.2833	8.4712	0.2477	-1.2803	0.4321	0.9883	-0.1347	-0.0404	-0.5378	0.6251	-0.113	-0.4539	-0.0076	-0.0776	-0.0687	-0.1527	-0.6742	-0.1512	9.0388	44.3991
6	7.0882	-1.0397	4.6677	3.8616	-0.4677	13.7567	0.0039	-0.603	0.2438	-0.3123	0.1243	-0.1787	-0.4861	0.1055	-0.1282	-0.8062	-0.0918	0.0166	-0.7825	-0.0544	-0.6382	4.1315	9.3833	8.2757
7	8.0535	1.9907	2.0989	4.1982	1.5401	10.6417	0.0835	-1.1249	-0.4176	0.8155	-0.2831	0.4507	1.1235	-0.852	0.1996	-0.4353	-0.0225	0.1853	-0.2265	0.1043	-0.3803	-16.8589	-4.127	39.9798
8	10.1833	2.7933	-1.8937	5.9993	0.5952	5.8501	-0.2737	0.0743	-0.4115	-0.4763	0.2391	-0.4245	0.4733	0.4128	0.0345	-0.6006	-0.0338	0.0222	-0.8005	0.0012	-0.6553	3.3173	-6.5335	8.3959

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	L	A	1 - 107	1 - 112
2	X-RAY DIFFRACTION	2	L	A	108 - 212	113 - 217
3	X-RAY DIFFRACTION	3	H	B	1 - 113	1 - 121
4	X-RAY DIFFRACTION	4	H	B	114 - 228	122 - 221
5	X-RAY DIFFRACTION	5	A	C	1 - 107	1 - 112
6	X-RAY DIFFRACTION	6	A	C	108 - 212	113 - 217
7	X-RAY DIFFRACTION	7	B	D	1 - 113	1 - 121
8	X-RAY DIFFRACTION	8	B	D	114 - 228	122 - 221

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