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- PDB-1wc7: FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1wc7
TitleFAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-L-ALANINE
Components
  • FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
  • FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
KeywordsANTIBODY / CATALYTIC ANTIBODY / TRANSAMINATION / PYRIDOXAL-PHOSPHATE / PHOSPHOPYRIDOXYL-L-ALANINE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IODIDE ION / ALANYL-PYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsGolinelli-Pimpaneau, B. / Christen, P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a Pseudomerohedrally Twinned Monoclinic Crystal Form of a Pyridoxal Phosphate-Dependent Catalytic Antibody
Authors: Golinelli-Pimpaneau, B.
#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 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: 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 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 1, 2024Group: 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 1.6Nov 13, 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)96,66910
Polymers95,7144
Non-polymers9556
Water2,144119
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)48,4315
Polymers47,8572
Non-polymers5743
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)48,2385
Polymers47,8572
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.476, 81.691, 79.330
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9997, 0.0248, -0.0076), (-0.0249, -0.9996, 0.0166), (-0.0072, 0.0167, 0.9998)57.1568, 3.485, -39.542
2given(-0.9996, 0.0204, -0.0193), (-0.0208, -0.9996, 0.019), (-0.0189, 0.0194, 0.9996)57.849, 3.276, -38.8874

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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.: 5 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-PP3 / ALANYL-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXYL-ALANINE-5-PHOSPHATE / VITAMIN B6 COMPLEXED WITH ALANINE


Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.91 Å3/Da / Density % sol: 35.8 %
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: ID14-3 / Wavelength: 0.931
DetectorDetector: 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: 34338 / % possible obs: 99.8 % / Redundancy: 3.31 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB 15A9 IN COMPLEX WITH PPL-L-LYSINE

15a9


Resolution: 2.33→20 Å / Num. parameters: 26448 / Num. restraintsaints: 35417 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 1713 5 %RANDOM
all0.2234 34285 --
obs0.2222 -98.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6611
Refinement stepCycle: LAST / Resolution: 2.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 26 119 6610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0.037
X-RAY DIFFRACTIONs_from_restr_planes0.0229
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0

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