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- PDB-2gfb: CRYSTAL STRUCTURE OF A CATALYTIC FAB HAVING ESTERASE-LIKE ACTIVITY -

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Basic information

Entry
Database: PDB / ID: 2gfb
TitleCRYSTAL STRUCTURE OF A CATALYTIC FAB HAVING ESTERASE-LIKE ACTIVITY
Components
  • IGG2A CNJ206 FAB (HEAVY CHAIN)
  • IGG2A CNJ206 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsGolinelli-Pimpaneau, B. / Knossow, M.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of a catalytic antibody Fab with esterase-like activity.
Authors: Golinelli-Pimpaneau, B. / Gigant, B. / Bizebard, T. / Navaza, J. / Saludjian, P. / Zemel, R. / Tawfik, D.S. / Eshhar, Z. / Green, B.S. / Knossow, M.
#1: Journal: Mol.Immunol. / Year: 1994
Title: Differences in the Biochemical Properties of Esterolytic Antibodies Correlate with Structural Diversity
Authors: Zemel, R. / Schindler, D.G. / Tawfik, D.S. / Eshhar, Z. / Green, B.S.
History
DepositionJul 7, 1994-
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGG2A CNJ206 FAB (LIGHT CHAIN)
B: IGG2A CNJ206 FAB (HEAVY CHAIN)
C: IGG2A CNJ206 FAB (LIGHT CHAIN)
D: IGG2A CNJ206 FAB (HEAVY CHAIN)
E: IGG2A CNJ206 FAB (LIGHT CHAIN)
F: IGG2A CNJ206 FAB (HEAVY CHAIN)
G: IGG2A CNJ206 FAB (LIGHT CHAIN)
H: IGG2A CNJ206 FAB (HEAVY CHAIN)
I: IGG2A CNJ206 FAB (LIGHT CHAIN)
J: IGG2A CNJ206 FAB (HEAVY CHAIN)
K: IGG2A CNJ206 FAB (LIGHT CHAIN)
L: IGG2A CNJ206 FAB (HEAVY CHAIN)
M: IGG2A CNJ206 FAB (LIGHT CHAIN)
N: IGG2A CNJ206 FAB (HEAVY CHAIN)
O: IGG2A CNJ206 FAB (LIGHT CHAIN)
P: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)374,86416
Polymers374,86416
Non-polymers00
Water0
1
A: IGG2A CNJ206 FAB (LIGHT CHAIN)
B: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-22 kcal/mol
Surface area18820 Å2
MethodPISA
2
C: IGG2A CNJ206 FAB (LIGHT CHAIN)
D: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area18750 Å2
MethodPISA
3
E: IGG2A CNJ206 FAB (LIGHT CHAIN)
F: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area18780 Å2
MethodPISA
4
G: IGG2A CNJ206 FAB (LIGHT CHAIN)
H: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-23 kcal/mol
Surface area18740 Å2
MethodPISA
5
I: IGG2A CNJ206 FAB (LIGHT CHAIN)
J: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area18840 Å2
MethodPISA
6
K: IGG2A CNJ206 FAB (LIGHT CHAIN)
L: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-23 kcal/mol
Surface area18780 Å2
MethodPISA
7
M: IGG2A CNJ206 FAB (LIGHT CHAIN)
N: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-23 kcal/mol
Surface area18770 Å2
MethodPISA
8
O: IGG2A CNJ206 FAB (LIGHT CHAIN)
P: IGG2A CNJ206 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,8582
Polymers46,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.700, 68.060, 83.660
Angle α, β, γ (deg.)71.90, 112.20, 119.60
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 141 / 3: CIS PROLINE - PRO B 149 / 4: CIS PROLINE - PRO B 151 / 5: CIS PROLINE - PRO B 200 / 6: CIS PROLINE - PRO C 8 / 7: CIS PROLINE - PRO C 141 / 8: CIS PROLINE - PRO D 149 / 9: CIS PROLINE - PRO D 151 / 10: CIS PROLINE - PRO D 200 / 11: CIS PROLINE - PRO E 8 / 12: CIS PROLINE - PRO E 141 / 13: CIS PROLINE - PRO F 149 / 14: CIS PROLINE - PRO F 151 / 15: CIS PROLINE - PRO F 200 / 16: CIS PROLINE - PRO G 8 / 17: CIS PROLINE - PRO G 141 / 18: CIS PROLINE - PRO H 149 / 19: CIS PROLINE - PRO H 151 / 20: CIS PROLINE - PRO H 200 / 21: CIS PROLINE - PRO I 8 / 22: CIS PROLINE - PRO I 141 / 23: CIS PROLINE - PRO J 149 / 24: CIS PROLINE - PRO J 151 / 25: CIS PROLINE - PRO J 200 / 26: CIS PROLINE - PRO K 8 / 27: CIS PROLINE - PRO K 141 / 28: CIS PROLINE - PRO L 149 / 29: CIS PROLINE - PRO L 151 / 30: CIS PROLINE - PRO L 200 / 31: CIS PROLINE - PRO M 8 / 32: CIS PROLINE - PRO M 141 / 33: CIS PROLINE - PRO N 149 / 34: CIS PROLINE - PRO N 151 / 35: CIS PROLINE - PRO N 200 / 36: CIS PROLINE - PRO O 8 / 37: CIS PROLINE - PRO O 141 / 38: CIS PROLINE - PRO P 149 / 39: CIS PROLINE - PRO P 151 / 40: CIS PROLINE - PRO P 200
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.52249, 0.01167, -0.85257), (-0.15299, -0.98496, 0.08027), (-0.83881, 0.17237, 0.51642)39.6062, 15.04773, 5.90891
2given(0.9994, 0.01652, 0.03053), (-0.01662, 0.99986, 0.00286), (-0.03047, -0.00337, 0.99953)14.50359, -6.66494, -38.9651
3given(-0.55038, -0.00422, -0.8349), (-0.14525, -0.98425, 0.10073), (-0.82218, 0.17671, 0.5411)64.35666, 14.17812, -31.27496
4given(0.99975, 0.01341, 0.01762), (-0.01339, 0.99991, -0.00151), (-0.01764, 0.00127, 0.99984)-99.1524, 1.15631, 1.51389
5given(-0.53447, 0.00263, -0.84518), (-0.15043, -0.98432, 0.09206), (-0.83169, 0.17635, 0.52649)93.4847, 29.82811, 87.38438
6given(0.99857, 0.02359, 0.04803), (-0.0242, 0.99963, 0.01219), (-0.04773, -0.01333, 0.99877)-85.6058, -4.57523, -34.4724
7given(-0.58233, -0.02994, -0.8124), (-0.13289, -0.98237, 0.13146), (-0.80202, 0.18452, 0.56809)121.9802, 24.8057, 45.7937
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS C AND D, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS E AND F, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS G AND H, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 4* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS I AND J, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 5* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS K AND L, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 6* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS M AND N, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 7* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS O AND P, RESPECTIVELY.

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Components

#1: Antibody
IGG2A CNJ206 FAB (LIGHT CHAIN)


Mass: 23502.881 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 12002892
#2: Antibody
IGG2A CNJ206 FAB (HEAVY CHAIN)


Mass: 23355.168 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 4091056
Sequence detailsRESIDUE NUMBERING IS ACCORDING TO KABAT (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN AND C. ...RESIDUE NUMBERING IS ACCORDING TO KABAT (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN AND C. FOELLER, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 1991). THIS RESIDUE NUMBERING DIFFERS FROM THE ONE USED IN THE PAPER IDENTIFYING THE DEPOSITED SET OF COORDINATES. THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS (RESIDUES 110 - 227) AND OF THE LIGHT CHAINS (RESIDUES 106 - 214) HAVE NOT BEEN DETERMINED FOR THIS IMMUNOGLOBULIN. THEY HAVE BEEN ASSIGNED THE CONSENSUS SEQUENCES FOR THE CONSTANT DOMAIN OF MOUSE KAPPA LIGHT CHAIN AND FOR THE FIRST CONSTANT DOMAIN OF MOUSE GROUP IIA HEAVY CHAINS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
217 %(w/v)PEG100001drop
320 %(v/v)glycerol1drop
40.1 MTris-HCl1drop
517 %(w/v)PEG100001reservoir
620 %(v/v)glycerol1reservoir
70.1 MTris-HCl1reservoir
80.15 M1reservoirNaCl
1protein1drop0.004ml

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 64830 / % possible obs: 93 % / Num. measured all: 115376 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.08 Å / Rmerge(I) obs: 0.143

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→7 Å / σ(F): 2
Details: RESIDUES 100A - 103 AND 128 - 136 OF THE HEAVY CHAINS ARE POORLY DEFINED BY THE ELECTRON DENSITY. CARE SHOULD ALSO BE EXERCISED IN INTERPRETING THIS MODEL, DUE TO THE LIMITED RESOLUTION. ...Details: RESIDUES 100A - 103 AND 128 - 136 OF THE HEAVY CHAINS ARE POORLY DEFINED BY THE ELECTRON DENSITY. CARE SHOULD ALSO BE EXERCISED IN INTERPRETING THIS MODEL, DUE TO THE LIMITED RESOLUTION. REFINEMENT AT HIGHER RESOLUTION IS PRESENTLY BEING PURSUED; IN THIS WORK, RESIDUE 114 OF THE HEAVY CHAIN, WHICH IS MISSING IN THIS ENTRY, HAS BEEN LOCATED, WHICH LEADS TO MODIFICATION OF THE ATOMIC POSITIONS OF THE SURROUNDING RESIDUES.
RfactorNum. reflection
Rwork0.213 -
obs0.213 64830
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26336 0 0 0 26336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2

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