PDB-1uwe: MOLECULAR MECHANISM OF ENANTIOSELECTIVE PROTON TRANSFER TO CARBON...

ID or keywords:

Entry

Database: PDB / ID: 1uwe

Title

MOLECULAR MECHANISM OF ENANTIOSELECTIVE PROTON TRANSFER TO CARBON IN CATALYTIC ANTIBODY 14D9

Components

(ANTIBODY 14D9) x 2

Keywords

ANTIBODY

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.67 Å

Authors

Baumann, U. / Reymond, J.L.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Molecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9
Authors: Zheng, L. / Baumann, U. / Reymond, J.L.

History

Deposition	Feb 5, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 27, 2004	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 15, 2017	Group: Source and taxonomy
Revision 1.3	Dec 13, 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1uwe.cif.gz	241.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1uwe.ent.gz	196.1 KB	Display	PDB format
PDBx/mmJSON format	1uwe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1uwe_validation.pdf.gz	402 KB	Display	wwPDB validaton report
Full document	1uwe_full_validation.pdf.gz	440 KB	Display
Data in XML	1uwe_validation.xml.gz	28.2 KB	Display
Data in CIF	1uwe_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uw/1uwe ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uwe	HTTPS FTP

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Related structure data

Related structure data	1uwgC 1d5iS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3qg7-d 4r4b-4 3fzu-2 1ngx-2 4lly-1 2xzc-d 5tjd-d 6y49-d 5xrq-1 4r7d-5 4kjp-3 4r7n-7 6arp-2 2o5z-d 6pds-1 6ju0-1 1rzi-5 6z3k-4 4yny-1 4odu-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

1uwgC

1d5iS

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

H: ANTIBODY 14D9

L: ANTIBODY 14D9

U: ANTIBODY 14D9

V: ANTIBODY 14D9

X: ANTIBODY 14D9

Y: ANTIBODY 14D9

137 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: ANTIBODY 14D9

L: ANTIBODY 14D9

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

2

U: ANTIBODY 14D9

V: ANTIBODY 14D9

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

3

X: ANTIBODY 14D9

Y: ANTIBODY 14D9

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

Unit cell

Length a, b, c (Å)	110.100, 142.790, 125.460
Angle α, β, γ (deg.)	90.00, 104.85, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	L
2	1	X
3	1	U
1	2	H
2	2	Y
3	2	V

NCS domain segments:

Refine code: 3

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	LEU	LEU	THR	THR	L	B	1 - 109	1 - 110
2	1	1	LEU	LEU	THR	THR	X	E	1 - 109	1 - 110
3	1	1	LEU	LEU	THR	THR	U	C	1 - 109	1 - 110
1	2	1	VAL	VAL	GLY	GLY	L	B	110 - 212	111 - 213
2	2	1	VAL	VAL	GLY	GLY	X	E	110 - 212	111 - 213
3	2	1	VAL	VAL	GLY	GLY	U	C	110 - 212	111 - 213
1	1	2	LEU	LEU	SER	SER	H	A	4 - 113	1 - 115
2	1	2	LEU	LEU	SER	SER	Y	F	4 - 113	1 - 115
3	1	2	LEU	LEU	SER	SER	V	D	4 - 113	1 - 115
1	2	2	SER	SER	CYS	CYS	H	A	115 - 216	117 - 218
2	2	2	SER	SER	CYS	CYS	Y	F	115 - 216	117 - 218
3	2	2	SER	SER	CYS	CYS	V	D	115 - 216	117 - 218

NCS ensembles :

ID
1
2

#1: Antibody	ANTIBODY 14D9 Mass: 22864.404 Da / Num. of mol.: 3 / Fragment: FAB HEAVY CHAIN, RESIDUES 4-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) Homo sapiens (human) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
#2: Antibody	ANTIBODY 14D9 Mass: 22940.182 Da / Num. of mol.: 3 / Fragment: FAB LIGHT CHAIN, RESIDUES 1-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) Homo sapiens (human) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.47 Å³/Da / Density % sol: 64.54 %

Crystal grow

pH: 4 / Details: PEG3350, CITRIC ACID, PH 3.5

Crystal grow

*PLUS

Temperature: 20 ℃ / pH: 3 / Method: vapor diffusion, sitting drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	8 %	PEG3350	1	reservoir
2	50 mM	citric acid	1	reservoir	pH3.0
3	20 mg/ml	Fab	1	drop
4	5 mM		1	drop		NaCl

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
Detector	Detector: CCD / Date: Jan 15, 2001
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.67→20 Å / Num. obs: 157522 / % possible obs: 93.8 % / Redundancy: 3.15 % / R_merge(I) obs: 0.035 / Net I/σ(I): 22.4
Reflection shell	Resolution: 2.67→2.83 Å / Redundancy: 3 % / R_merge(I) obs: 0.172 / Mean I/σ(I) obs: 5.4 / % possible all: 77.6
Reflection	PLUS Highest resolution: 2.67 Å / Lowest resolution: 20 Å / Num. obs: 49857 / Num. measured all: 157522 / R_merge(I) obs*: 0.035
Reflection shell	PLUS % possible obs: 77.6 % / R_merge(I) obs: 0.172 / Mean I/σ(I) obs*: 5.4

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
XDS		data reduction
XSCALE		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D5I

1d5i

Resolution: 2.67→20 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.897 / SU B: 11.93 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.549 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.271	1530	3 %	RANDOM
R_work	0.218	-	-	-
obs	0.219	49895	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 9.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.15 Å²	0 Å²	1.15 Å²
2-	-	-0.76 Å²	0 Å²
3-	-	-	-2.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.67→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9678	0	0	25	9703

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	9927
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.005	1.938	13569
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.485	5	1287
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1551
X-RAY DIFFRACTION	r_gen_planes_refined	0.001	0.02	7572
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.267	0.2	3935
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	360
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	0.468	0.2	95
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.319	0.2	8
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	0.328	1	6435
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.676	1	10407
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.789	1.5	3492
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.228	4.5	3162
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	L	852	tight positional	0.08	0.05
1	2	X	852	tight positional	0.08	0.05
1	3	U	852	tight positional	0.11	0.05
2	1	H	868	tight positional	0.16	0.05
2	2	Y	868	tight positional	0.12	0.05
2	3	V	868	tight positional	0.13	0.05
1	1	L	762	loose positional	0.37	5
1	2	X	762	loose positional	0.37	5
1	3	U	762	loose positional	0.37	5
2	1	H	739	loose positional	0.75	5
2	2	Y	739	loose positional	0.53	5
2	3	V	739	loose positional	0.5	5
1	1	L	852	tight thermal	0.19	0.5
1	2	X	852	tight thermal	0.18	0.5
1	3	U	852	tight thermal	0.2	0.5
2	1	H	868	tight thermal	0.18	0.5
2	2	Y	868	tight thermal	0.21	0.5
2	3	V	868	tight thermal	0.24	0.5
1	1	L	762	loose thermal	1.54	10
1	2	X	762	loose thermal	1.43	10
1	3	U	762	loose thermal	1.72	10
2	1	H	739	loose thermal	1.81	10
2	2	Y	739	loose thermal	1.65	10
2	3	V	739	loose thermal	2.09	10

LS refinement shell

Resolution: 2.67→2.74 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.407	92
R_work	0.332	3589

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	6.6135	-3.9689	4.9962	9.3929	-4.8799	5.2526	-0.6915	-0.718	0.6259	1.6808	0.0657	-1.5612	-0.9433	0.3841	0.6258	0.5161	-0.0178	-0.4841	0.869	-0.0442	1.0292	50.343	62.685	43.186
2	4.7938	5.8624	2.5101	11.8203	1.583	4.5589	-0.1622	-0.0315	-0.2489	-0.5743	0.2922	0.5834	0.3691	-0.5379	-0.1301	0.3301	-0.2068	-0.0976	0.6111	0.0468	0.5739	23.367	52.933	19.154
3	12.0331	6.4563	3.4352	11.5799	0.6635	3.1506	-0.1847	-0.1753	-1.5348	1.1413	0.3072	-2.4787	0.4759	0.5637	-0.1226	0.5517	0.1881	-0.2797	0.9544	0.2358	1.5532	54.498	40.91	42.326
4	4.9104	2.6271	-2.3339	11.4936	-5.5032	8.8393	-0.3024	0.6638	-0.4974	-1.7564	0.0861	-0.5813	0.6377	0.2782	0.2163	0.619	-0.0726	0.1631	0.6572	-0.1266	0.7447	36.571	44.757	16.963
5	7.9339	-3.5572	-5.1135	7.4629	2.6311	5.2407	0.5006	0.4672	1.1433	-0.56	-0.0415	-0.3309	-0.8122	-0.3774	-0.4591	0.459	-0.098	-0.052	0.5736	0.061	0.9186	11.85	54.15	44.436
6	8.219	3.3854	-1.5882	12.6128	-2.153	3.8561	-0.3898	0.45	-1.0137	-0.5226	0.0003	-0.3921	1.2129	-0.169	0.3895	0.6831	-0.1134	0.0251	0.5058	-0.0654	0.7234	19.69	17.587	42.751
7	5.6774	1.4167	-0.7184	10.5741	0.2296	7.697	0.1561	-0.4548	1.1556	0.4731	-0.1549	0.233	-0.6281	-0.6629	-0.0012	0.2451	-0.0628	-0.087	0.8399	-0.1762	0.6963	-2.379	47.2	59.891
8	19.9349	0.2625	-1.1932	4.9675	0.3034	4.1633	-0.4898	-1.5217	-0.6573	0.6777	0.2286	-0.7057	1.0134	0.7595	0.2613	0.6696	-0.0871	-0.2313	0.7639	0.0564	0.4394	16.498	22.346	57.301
9	2.9086	1.6185	-1.3307	2.2338	-0.2392	11.5573	0.4492	-0.4545	0.0458	0.252	-0.2788	-0.2518	-0.4618	1.0843	-0.1704	0.3764	-0.1706	-0.105	0.505	-0.0113	0.3783	57.828	95.512	22.413
10	8.7248	5.8947	-2.1109	7.6536	-0.249	7.4565	0.2971	-0.3218	-0.0574	0.79	-0.2524	0.4121	0.5358	-0.4862	-0.0447	0.5093	-0.1768	0.0037	0.5789	-0.0983	0.4103	33.398	82.663	47.472
11	5.7376	3.9569	-3.6674	6.4459	-2.4326	7.8633	0.2183	0.4023	0.3055	-0.3024	-0.0166	0.3198	-0.4005	-0.5249	-0.2018	0.3076	0.0459	-0.1409	0.4545	-0.0037	0.3719	41.52	89.911	8.526
12	2.728	0.4763	1.0202	9.1505	5.1368	8.4509	-0.1471	-0.4064	0.6332	0.4495	-0.325	0.9324	-0.7259	-1.3404	0.4721	0.4214	0.1257	-0.0448	0.711	-0.0755	0.6515	26.141	90.168	35.66

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	L	1 - 109
2	X-RAY DIFFRACTION	2	L	110 - 212
3	X-RAY DIFFRACTION	3	H	4 - 113
4	X-RAY DIFFRACTION	4	H	114 - 216
5	X-RAY DIFFRACTION	5	X	1 - 109
6	X-RAY DIFFRACTION	6	X	110 - 212
7	X-RAY DIFFRACTION	7	Y	4 - 113
8	X-RAY DIFFRACTION	8	Y	114 - 216
9	X-RAY DIFFRACTION	9	U	1 - 109
10	X-RAY DIFFRACTION	10	U	110 - 212
11	X-RAY DIFFRACTION	11	V	4 - 113
12	X-RAY DIFFRACTION	12	V	114 - 216

Refinement

*PLUS

Lowest resolution: 20 Å / R_factor R_free: 0.27 / R_factor R_work: 0.216

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Type: r_bond_d / Dev ideal: 0.006

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