PDB-2ai0: Anti-Cocaine Antibody 7.5.21, Crystal Form III

Basic information

• Entry: Database: PDB / ID: 2ai0
• Title: Anti-Cocaine Antibody 7.5.21, Crystal Form III

Components

• Immunoglobulin Heavy Chain
• Immunoglobulin Light Chain kappa

• Keywords: IMMUNE SYSTEM

Function / homology

Domain/homology:

Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta

Component:

Igh protein

• Biological species: Mus musculus (house mouse)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
• Authors: Pozharski, E. / Hewagama, A. / Shanafelt, A. / Ringe, D. / Petsko, G.A.
• Citation: Journal: To be Published; Title: Flexibility of Packing: Four Crystal Forms of an Anti-Cocaine Antibody 7.5.21; Authors: Pozharski, E. / Hewagama, A. / Shanafelt, A. / Ringe, D. / Petsko, G.A.

History

Deposition	Jul 28, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Aug 23, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• 196 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	195,693	39
Polymers	192,731	8
Non-polymers	2,962	31
Water	9,566	531

1

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by author&software
• 49 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	49,039	11
Polymers	48,183	2
Non-polymers	857	9
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	4600 Å2
ΔGint	-77 kcal/mol
Surface area	20450 Å2
Method	PISA

2

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by author&software
• 49 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	49,043	11
Polymers	48,183	2
Non-polymers	861	9
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	5090 Å2
ΔGint	-119 kcal/mol
Surface area	20460 Å2
Method	PISA

3

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by author&software
• 48.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,755	8
Polymers	48,183	2
Non-polymers	572	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	4600 Å2
ΔGint	-80 kcal/mol
Surface area	20010 Å2
Method	PISA

4

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by author&software
• 48.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,855	9
Polymers	48,183	2
Non-polymers	672	7
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	4430 Å2
ΔGint	-90 kcal/mol
Surface area	19940 Å2
Method	PISA

5

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

hetero molecules

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 196 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	195,693	39
Polymers	192,731	8
Non-polymers	2,962	31
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
crystal symmetry operation	3_545	-x+1/2,y-1/2,-z	1
crystal symmetry operation	3_554	-x+1/2,y+1/2,-z-1	1
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	24300 Å2
ΔGint	-451 kcal/mol
Surface area	75270 Å2
Method	PISA

6

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

hetero molecules

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 196 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	195,693	39
Polymers	192,731	8
Non-polymers	2,962	31
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	2_546	-x,-y-1,z+1	1
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	22930 Å2
ΔGint	-417 kcal/mol
Surface area	76650 Å2
Method	PISA

7

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

hetero molecules

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 196 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	195,693	39
Polymers	192,731	8
Non-polymers	2,962	31
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
crystal symmetry operation	2_554	-x,-y,z-1	1
crystal symmetry operation	2_545	-x,-y-1,z	1
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	23030 Å2
ΔGint	-408 kcal/mol
Surface area	76540 Å2
Method	PISA

8

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 196 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	195,693	39
Polymers	192,731	8
Non-polymers	2,962	31
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1

Calculated values:

Buried area	22450 Å2
ΔGint	-429 kcal/mol
Surface area	77130 Å2
Method	PISA

9

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 97.9 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	97,899	20
Polymers	96,366	4
Non-polymers	1,533	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	11060 Å2
ΔGint	-218 kcal/mol
Surface area	38860 Å2
Method	PISA

10

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

hetero molecules

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 97.8 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	97,795	19
Polymers	96,366	4
Non-polymers	1,429	15
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_566	x,y+1,z+1	1

Calculated values:

Buried area	10810 Å2
ΔGint	-187 kcal/mol
Surface area	38850 Å2
Method	PISA

11

N: Immunoglobulin Light Chain kappa

J: Immunoglobulin Heavy Chain

hetero molecules

O: Immunoglobulin Light Chain kappa

K: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 97.6 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	97,610	17
Polymers	96,366	4
Non-polymers	1,245	13
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_544	-x+1/2,y-1/2,-z-1	1

Calculated values:

Buried area	10270 Å2
ΔGint	-197 kcal/mol
Surface area	38700 Å2
Method	PISA

12

M: Immunoglobulin Light Chain kappa

I: Immunoglobulin Heavy Chain

hetero molecules

L: Immunoglobulin Light Chain kappa

H: Immunoglobulin Heavy Chain

hetero molecules

Summary:

• defined by software
• 98.1 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,083	22
Polymers	96,366	4
Non-polymers	1,717	18
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_545	-x+1/2,y-1/2,-z	1

Calculated values:

Buried area	10870 Å2
ΔGint	-215 kcal/mol
Surface area	39730 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	159.979, 216.355, 58.320
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P21212

Components on special symmetry positions

ID	Model	Components
1	1	K-696- HOH

Components

#1: Antibody

L M N O
Immunoglobulin Light Chain kappa

Details:

Mass: 24035.725 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / Strain: BALB/C

#2: Antibody

H I J K
Immunoglobulin Heavy Chain /

Details:

Mass: 24147.045 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / Strain: BALB/C / References: UniProt: Q6PIP8

#3: Chemical

L-602 L-609 L-612 L-625 H-605 H-610 H-623 M-603 M-604 M-606 M-608 M-614 M-622 I-618 I-620 N-601 N-613 N-615 J-616 J-624 ...
ChemComp-SO4 / SULFATE ION / Sulfate

Details:

Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO₄

#4: Chemical

L-702 L-704 I-701 N-703
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol

Details:

Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃

#5: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.6 ų/Da / Density % sol: 52.8 %
• Crystal grow: Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 ; Details: 16% PEG8000, 0.3M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Data collection

• Diffraction: Mean temperature: 105 K
• Diffraction source: Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.89996 Å
• Detector: Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2004
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.89996 Å / Relative weight: 1
• Reflection: Resolution: 2.2→50 Å / Num. all: 101629 / Num. obs: 101629 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / B_iso Wilson estimate: 47.6 Ų / R_merge(I) obs: 0.059 / Χ²: 1.099 / Net I/σ(I): 26.7
• Reflection shell: Resolution: 2.2→2.28 Å / % possible obs: 91.6 % / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.8 / Num. measured obs: 9380 / Num. unique all: 9380 / Χ²: 1.217 / % possible all: 91.6

Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	1.7	data extraction
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A1W, constant and variable domains used separately

2a1w

Resolution: 2.2→129.1 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.92 / SU B: 15.307 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.279	5097	5 %	RANDOM
Rwork	0.222	-	-	-
all	0.225	101532	-	-
obs	-	101532	97.77 %	-

• 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: 48.205 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.86 Å2	0 Å2	0 Å2
2-	-	0.47 Å2	0 Å2
3-	-	-	-1.33 Å2

Refinement step

Cycle: LAST / Resolution: 2.2→129.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13384	0	159	531	14074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	13864
X-RAY DIFFRACTION	r_angle_refined_deg	1.342	1.961	18880
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.749	5	1733
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.71	23.413	545
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.69	15	2178
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.555	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	2081
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10384
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	5695
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	9063
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	761
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.194	0.2	111
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.141	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	0.544	1.5	8887
X-RAY DIFFRACTION	r_mcangle_it	0.935	2	14085
X-RAY DIFFRACTION	r_scbond_it	1.28	3	5735
X-RAY DIFFRACTION	r_scangle_it	1.93	4.5	4795

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.37	367	-
Rwork	0.295	6547	-
all	-	6914	-
obs	-	6547	91.21 %

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	0.9858	-0.6029	0.5268	1.91	-0.631	2.0392	-0.0958	0.0478	-0.0264	0.0513	0.0857	-0.1649	-0.1879	0.0146	0.0101	-0.1133	-0.0046	0.0163	-0.1442	-0.1073	-0.0309	22.9038	39.7244	9.4209
2	0.9897	-0.6464	0.3866	3.3217	-0.8656	3.0886	0.0131	-0.1725	-0.0778	0.249	0.1384	0.3667	0.0754	0.0844	-0.1514	-0.0924	0.0275	0.0382	-0.0717	-0.0233	-0.0835	12.4766	67.4674	28.1167
3	0.5044	-0.4881	0.8799	1.457	-0.2958	2.3454	-0.0754	-0.0429	-0.1144	-0.0582	0.101	-0.1535	-0.0753	0.0914	-0.0256	-0.2083	0.0479	0.041	-0.1115	-0.088	0.3032	23.7122	-67.6581	-21.2369
4	2.6959	-1.1765	0.4124	2.4806	-1.0451	2.443	0.1662	0.0246	-0.5614	0.1174	0.0115	0.4383	0.0789	0.5253	-0.1777	-0.2508	-0.0116	-0.0043	-0.1557	-0.0538	-0.0787	12.6741	-38.649	-3.0365
5	0.933	0.5666	-0.6306	2.7098	0.5981	3.5409	-0.0745	-0.0564	0.2727	0.2626	-0.1924	0.1204	0.2512	-0.1642	0.2669	-0.1716	-0.033	0.0747	-0.0655	-0.0644	0.108	24.5553	-99.1379	-39.6636
6	1.028	0.2357	-0.5804	3.287	-1.9734	3.533	0.0678	0.3477	0.0496	-0.5844	0.0763	0.2478	0.2461	0.1504	-0.1442	0.0316	-0.1114	0.004	-0.0259	-0.0164	-0.2115	16.2008	-127.2434	-59.6662
7	0.9991	0.0197	-0.7705	1.2591	-0.1423	3.6044	-0.1184	-0.0241	0.1198	-0.2	0.046	-0.1274	0.1289	0.0048	0.0724	-0.0934	-0.0291	0.0706	-0.2509	-0.0722	-0.1617	20.2332	9.9528	-12.0925
8	0.3671	0.2251	-0.4968	1.9098	-1.4323	3.617	0.1367	0.0662	-0.1132	-0.2621	-0.1107	0.0003	0.1424	0.4992	-0.0261	-0.0122	-0.1034	0.0144	0.0382	-0.0377	-0.2263	14.0912	-17.086	-32.5857

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	L	A	1 - 112	1 - 112
2	1	H	B	1 - 123	1 - 123
3	2	L	A	113 - 216	113 - 216
4	2	H	B	124 - 224	124 - 224
5	3	M	C	1 - 112	1 - 112
6	3	I	D	1 - 123	1 - 123
7	4	M	C	113 - 216	113 - 216
8	4	I	D	124 - 223	124 - 223
9	5	N	E	1 - 112	1 - 112
10	5	J	F	1 - 123	1 - 123
11	6	N	E	113 - 216	113 - 216
12	6	J	F	124 - 223	124 - 223
13	7	O	G	1 - 112	1 - 112
14	7	K	H	1 - 123	1 - 123
15	8	O	G	113 - 216	113 - 216
16	8	K	H	124 - 223	124 - 223