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- PDB-43ca: CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9... -

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Basic information

Entry
Database: PDB / ID: 43ca
TitleCRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY WITH BOUND P-NITROPHENOL
Components
  • PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
  • PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
KeywordsIMMUNOGLOBULIN / CATALYTIC ANTIBODY
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
P-NITROPHENOL / Ig heavy chain V region PJ14 / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsThayer, M.M. / Getzoff, E.D. / Roberts, V.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structural basis for amide hydrolysis catalyzed by the 43C9 antibody.
Authors: Thayer, M.M. / Olender, E.H. / Arvai, A.S. / Koike, C.K. / Canestrelli, I.L. / Stewart, J.D. / Benkovic, S.J. / Getzoff, E.D. / Roberts, V.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Catalytic antibody model and mutagenesis implicate arginine in transition-state stabilization.
Authors: Roberts, V.A. / Stewart, J. / Benkovic, S.J. / Getzoff, E.D.
#2: Journal: Biochemistry / Year: 1994
Title: Site-directed mutagenesis of a catalytic antibody: an arginine and a histidine residue play key roles.
Authors: Stewart, J.D. / Roberts, V.A. / Thomas, N.R. / Getzoff, E.D. / Benkovic, S.J.
History
DepositionMar 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
B: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
C: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
D: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
E: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
F: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
G: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
H: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,45412
Polymers100,8978
Non-polymers5564
Water2,972165
1
A: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
B: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3633
Polymers25,2242
Non-polymers1391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
D: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3633
Polymers25,2242
Non-polymers1391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
F: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3633
Polymers25,2242
Non-polymers1391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
H: PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3633
Polymers25,2242
Non-polymers1391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.250, 110.860, 244.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.04082, 0.99916, -0.00256), (0.99913, 0.04084, 0.00901), (0.0091, -0.00219, -0.99996)-1.06637, 0.81899, 60.60689
2given(-0.13755, -0.85875, 0.49359), (-0.87524, -0.12792, -0.46646), (0.46372, -0.49617, -0.73402)43.66117, 143.29333, 37.76854
3given(-0.88101, -0.15082, -0.44841), (-0.07226, -0.8938, 0.4426), (-0.46754, 0.42234, 0.77655)110.16896, 71.012, 38.68391
4given(-0.04058, 0.99917, -0.00219), (0.99898, 0.04062, 0.01953), (0.0196, -0.0014, -0.99981)-1.00269, 0.51454, 60.11622
5given(-0.133, -0.86795, 0.47852), (-0.8673, -0.13176, -0.48004), (0.4797, -0.47886, -0.73524)44.42468, 143.49197, 35.68245
6given(-0.88177, -0.15436, -0.4457), (-0.07449, -0.8875, 0.45474), (-0.46576, 0.43418, 0.77108)110.11682, 70.72927, 38.28638
7given(-0.03765, 0.99929, -0.00085), (0.99916, 0.03766, 0.01636), (0.01638, -0.00024, -0.99987)-1.23821, 0.65705, 60.28713
8given(-0.13648, -0.86321, 0.48606), (-0.86931, -0.13093, -0.47661), (0.47505, -0.48758, -0.73253)44.12121, 143.41975, 36.32618
9given(-0.88224, -0.14713, -0.44723), (-0.07863, -0.89053, 0.44808), (-0.4642, 0.43048, 0.77409)110.09941, 71.34642, 38.13198

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Components

#1: Antibody
PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))


Mass: 12434.939 Da / Num. of mol.: 4 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERZ9
#2: Antibody
PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))


Mass: 12789.393 Da / Num. of mol.: 4 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P01820
#3: Chemical
ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHERE IS ONE P-NITROPHENOL FRAGMENT FOR EACH FV.
Sequence detailsTHE FV FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT, E. A. KABAT, T. T. WU, H. M. PERRY, K. S. ...THE FV FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT, E. A. KABAT, T. T. WU, H. M. PERRY, K. S. GOTTESMAN, C. FOELLER, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, FIFTH EDITION, (1991), U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES, WASHINGTON,

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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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growpH: 7 / Details: 80% NACL, 50 MM MOPS PH 6.5, pH 7.00
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
170-80 %1reservoirNaCl
250 mMMOPS1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 52873 / % possible obs: 82.1 % / Redundancy: 3 % / Biso Wilson estimate: 53.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.12 / Rsym value: 0.294 / % possible all: 0.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / % possible obs: 82.1 % / Redundancy: 3 % / Num. measured all: 158471 / Rmerge(I) obs: 0.078 / Biso Wilson estimate: 53.1 Å2
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.12

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.3→35 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE FLEXIBLE LINKER BETWEEN THE LIGHT AND HEAVY CHAINS WAS NOT OBSERVED IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2633 4.09 %RANDOM
Rwork0.206 ---
obs-51960 80.79 %-
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---6.96 Å20 Å2
3----24.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7066 0 40 165 7271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.69
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
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.437 82 1.03 %
Rwork0.39 1651 -
obs--21.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMH19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARHAPTEN.PROTOPHAPTEN.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35 Å / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.437 / Rfactor Rwork: 0.39

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