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- PDB-1kno: CRYSTAL STRUCTURE OF THE COMPLEX OF A CATALYTIC ANTIBODY FAB WITH... -

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Basic information

Entry
Database: PDB / ID: 1kno
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF A CATALYTIC ANTIBODY FAB WITH A TRANSITION STATE ANALOG: STRUCTURAL SIMILARITIES IN ESTERASE-LIKE ABZYMES
Components(IGG2A FAB FRAGMENT CNJ206) x 2
KeywordsCATALYTIC ANTIBODY
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / extracellular region / plasma membrane
Similarity search - Function
: / : / 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 ...: / : / 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
Similarity search - Domain/homology
Chem-PNP / : / : / Immunoglobulin kappa constant / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsCharbonnier, J.-B. / Gigant, B. / Knossow, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.
Authors: Charbonnier, J.B. / Carpenter, E. / Gigant, B. / Golinelli-Pimpaneau, B. / 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.
#2: 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.
History
DepositionSep 11, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG2A FAB FRAGMENT CNJ206
B: IGG2A FAB FRAGMENT CNJ206
C: IGG2A FAB FRAGMENT CNJ206
D: IGG2A FAB FRAGMENT CNJ206
E: IGG2A FAB FRAGMENT CNJ206
F: IGG2A FAB FRAGMENT CNJ206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,72010
Polymers141,0046
Non-polymers7174
Water00
1
A: IGG2A FAB FRAGMENT CNJ206
B: IGG2A FAB FRAGMENT CNJ206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2844
Polymers47,0012
Non-polymers2832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-25 kcal/mol
Surface area18790 Å2
MethodPISA
2
C: IGG2A FAB FRAGMENT CNJ206
D: IGG2A FAB FRAGMENT CNJ206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2183
Polymers47,0012
Non-polymers2171
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-25 kcal/mol
Surface area18740 Å2
MethodPISA
3
E: IGG2A FAB FRAGMENT CNJ206
F: IGG2A FAB FRAGMENT CNJ206
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2183
Polymers47,0012
Non-polymers2171
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-25 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 76.900, 88.300
Angle α, β, γ (deg.)93.80, 93.90, 115.60
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 157 / 4: CIS PROLINE - PRO B 159 / 5: CIS PROLINE - PRO B 208 / 6: CIS PROLINE - PRO C 8 / 7: CIS PROLINE - PRO C 141 / 8: CIS PROLINE - PRO D 157 / 9: CIS PROLINE - PRO D 159 / 10: CIS PROLINE - PRO D 208 / 11: CIS PROLINE - PRO E 8 / 12: CIS PROLINE - PRO E 141 / 13: CIS PROLINE - PRO F 157 / 14: CIS PROLINE - PRO F 159 / 15: CIS PROLINE - PRO F 208
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.48054, -0.87671, 0.02133), (-0.87658, 0.47945, -0.04163), (0.02627, -0.0387, -0.99891)36.70313, -58.11688, 37.8546
2given(0.17898, -0.69453, -0.69685), (-0.69727, -0.58924, 0.40819), (-0.69411, 0.41283, -0.58974)24.79183, 34.48792, 7.39009
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 C 1 .. D 235 A 1 .. B 235 0.507 M2 E 1 .. F 235 A 1 .. B 235 0.453

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Components

#1: Antibody IGG2A FAB FRAGMENT CNJ206


Mass: 23574.941 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: GenBank: 12002892, UniProt: P01837*PLUS
#2: Antibody IGG2A FAB FRAGMENT CNJ206


Mass: 23426.248 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: GenBank: 4091056, UniProt: P01863*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PNP / METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER / 4-NITROPHENYL HYDROGEN METHYLPHOSPHONATE


Mass: 217.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8NO5P
Has protein modificationY
Sequence detailsRESIDUE NUMBERING FOLLOWS THE ORDER OF APPEARANCE IN THE SEQUENCE. THIS NUMBERING CORRESPONDS TO ...RESIDUE NUMBERING FOLLOWS THE ORDER OF APPEARANCE IN THE SEQUENCE. THIS NUMBERING CORRESPONDS TO 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein 1drop
28 %(w/v)PEG100001drop
317 %(v/v)glycerol1drop
40.5 mM1dropZnSO4
51 mMhapten 31drop
60.1 MTris-HCl1drop
70.05 %1dropNaN3
88 %(w/v)PEG100001reservoir
917 %(v/v)glycerol1reservoir
100.5 mM1reservoirZnSO4
110.1 MTris-HCl1reservoir
120.05 %1reservoirNaN3
130.15 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 1994 / Details: BENT MIRROR
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 27401 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.112
Reflection
*PLUS
Rmerge(I) obs: 0.112
Reflection shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / % possible obs: 89 %

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Processing

Software
NameVersionClassification
MOSFLM5.2data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3.2→7 Å / σ(F): 2
Details: RESIDUES 212 - 214 OF THE LIGHT CHAINS AND 136 - 144, 234 - 235 OF THE HEAVY CHAINS ARE POORLY DEFINED BY THE ELECTRON DENSITY. CARE SHOULD ALSO BE EXERCISED IN INTERPRETING THIS MODEL, DUE ...Details: RESIDUES 212 - 214 OF THE LIGHT CHAINS AND 136 - 144, 234 - 235 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.
RfactorNum. reflection% reflection
Rfree0.272 -10 %
Rwork0.2 --
obs0.2 18983 96 %
Displacement parametersBiso mean: 34.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 43 0 9949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg1.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
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: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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