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- PDB-2bmk: Fab fragment of PLP-dependent catalytic antibody 15A9 in complex ... -

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Basic information

Entry
Database: PDB / ID: 2bmk
TitleFab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine
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 / N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMar 14, 2005Deposition 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 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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)97,11612
Polymers95,7144
Non-polymers1,4028
Water6,377354
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)48,5586
Polymers47,8572
Non-polymers7014
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)48,5586
Polymers47,8572
Non-polymers7014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.152, 81.152, 79.331
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9993, 0.0291, 0.0243), (0.0296, -0.9994, -0.0202), (0.0237, 0.0209, -0.9995)-8.8692, 118.2019, 116.8956
2given(0.9993, 0.0368, 0.0113), (0.037, -0.9992, -0.0177), (0.0107, 0.0181, -0.9998)-8.2504, 117.5148, 117.5231

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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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-PDD / N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE


Type: D-peptide linking / Mass: 320.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.8 Å3/Da / Density % sol: 32.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 30%PEG 3350, 200MM SODIUM IODIDE, 50MM SODIUM ACETATE, PH6, VAPOR DIFFUSION, TEMPERATURE 298K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 32263 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.06 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

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

1wcb


Resolution: 2.3→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 3220 9 %RANDOM
Rwork0.2097 ---
obs0.2097 32247 90.2 %-
Solvent computationBsol: 37.74 Å2 / ksol: 0.328199 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.029 Å20 Å20.337 Å2
2---3.531 Å20 Å2
3---3.503 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 48 354 6967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006802
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_deg1.37936
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: 2.3→2.4 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.3826 107
Rwork0.3152 275
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PPD.PARPPD.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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