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- PDB-1wcb: PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN -

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Basic information

Entry
Database: PDB / ID: 1wcb
TitlePLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN
Components
  • FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
  • FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / CATALYTIC ANTIBODY / TRANSAMINATION / PYRIDOXAL-PHOSPHATE / HAPTEN / PHOSPHOPYRIDOXYL-L-LYSINE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IODIDE ION / Chem-PE1
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGolinelli-Pimpaneau, B. / Christen, P.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structural Basis for D-Amino Acid Transamination by the Pyridoxal- 5' -Phosphate - Dependent Catalytic Antibody 15A9.
Authors: Golinelli-Pimpaneau, B. / Luthi, C. / Christen, P.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Monoclonal Antibodies Against N-Alpha-(5'-Phosphopyridoxyl)-L-Lysine.
Authors: Gramatikova, S.I. / Christen, P.
History
DepositionNov 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: 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 ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
B: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
H: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
L: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,61115
Polymers95,7144
Non-polymers1,89711
Water8,521473
1
A: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
B: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7427
Polymers47,8572
Non-polymers8855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
L: FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8698
Polymers47,8572
Non-polymers1,0126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.900, 60.300, 64.600
Angle α, β, γ (deg.)79.40, 78.20, 80.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2438, -0.9679, -0.0609), (-0.9695, 0.2448, -0.0102), (0.0248, 0.0566, -0.9981)63.798, 96.468, 54.511
2given(-0.2405, -0.9682, -0.0693), (-0.9703, 0.2418, -0.0116), (0.028, 0.0645, -0.9975)63.934, 96.721, 54.122

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Components

#1: Antibody FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN


Mass: 23355.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 15A9 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) / Strain (production host): BALB/C
#2: Antibody FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN


Mass: 24501.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): 15A9 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) / Strain (production host): BALB/C
#3: Chemical ChemComp-PE1 / N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE / PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE


Type: L-peptide linking / Mass: 377.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N3O7P
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 3350, 200MM SODIUM REMARK 280 IODIDE, 50MM SODIUM ACETATE, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 28522 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.1 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLO

1clo


Resolution: 2.5→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY: ALA H 129, ALA H 130, ARG H 213, ASP H 214, ALA B 129, ALA B 130 THE SIDE-CHAINS OF THE FOLLOWING RESIDUES ARE POORLY DEFINED ...Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY: ALA H 129, ALA H 130, ARG H 213, ASP H 214, ALA B 129, ALA B 130 THE SIDE-CHAINS OF THE FOLLOWING RESIDUES ARE POORLY DEFINED BY THE ELECTRON DENSITY AND WERE MODELLED AS ALANINE: SER L 56, LYS L 142, LYS H 43, ARG H 83, GLU H 100C, GLN H 131, SER H 134, SER H 158, GLN H 171, GLU H 191, LYS H 205, LYS H 209, GLN B 131, SER B 134, GLN B 171, LYS B 209
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 2818 9.8 %RANDOM
Rwork0.223 ---
obs0.223 28273 98.1 %-
Solvent computationBsol: 36.4942 Å2 / ksol: 0.332759 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.313 Å22.169 Å20.419 Å2
2---2.401 Å20.179 Å2
3---2.713 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6635 0 59 473 7167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.07502
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.43637
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.52 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3937 50 9.45 %
Rwork0.2927 479 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PPE.PARPPE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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