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- PDB-5xqw: Catalytic antibody 7B9 -

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Basic information

Entry
Database: PDB / ID: 5xqw
TitleCatalytic antibody 7B9
Components
  • Fab fragment of catalytic antibody 7B9, heavy chain
  • Fab fragment of catalytic antibody 7B9, light chain
KeywordsIMMUNE SYSTEM / catalytic antibody / hydrolytic enzyme / Fab / transition-state analogue
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ethyl-[(4-nitrophenyl)methoxy]phosphinic acid
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIto, N. / Fujii, I. / Tsumuraya, T.
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters.
Authors: Miyamoto, N. / Yoshimura, M. / Okubo, Y. / Suzuki-Nagata, K. / Tsumuraya, T. / Ito, N. / Fujii, I.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab fragment of catalytic antibody 7B9, light chain
H: Fab fragment of catalytic antibody 7B9, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7933
Polymers46,5482
Non-polymers2451
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.942, 61.904, 70.959
Angle α, β, γ (deg.)90.00, 92.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab fragment of catalytic antibody 7B9, light chain


Mass: 23231.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab fragment of catalytic antibody 7B9, heavy chain


Mass: 23315.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-8EU / ethyl-[(4-nitrophenyl)methoxy]phosphinic acid


Mass: 245.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris HCl, 15%(w/v) PEG 1000, 5% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Apr 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 19632 / % possible obs: 98.8 % / Redundancy: 2.6 % / Rsym value: 0.04 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.324 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KB5

1kb5


Resolution: 2.2→14.97 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.995 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26082 1930 9.8 %RANDOM
Rwork0.18748 ---
obs0.19453 17702 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å2-0 Å2-1.16 Å2
2---1.48 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 2.2→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 16 54 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023308
X-RAY DIFFRACTIONr_bond_other_d0.0020.022975
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9524497
X-RAY DIFFRACTIONr_angle_other_deg0.95336908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49524.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39515531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.676159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7224.8281680
X-RAY DIFFRACTIONr_mcbond_other3.7214.8271679
X-RAY DIFFRACTIONr_mcangle_it5.2647.2212093
X-RAY DIFFRACTIONr_mcangle_other5.2637.2212094
X-RAY DIFFRACTIONr_scbond_it3.9545.1271628
X-RAY DIFFRACTIONr_scbond_other3.9565.1281625
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7987.5432402
X-RAY DIFFRACTIONr_long_range_B_refined7.8838.2093514
X-RAY DIFFRACTIONr_long_range_B_other7.88338.213511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 118 -
Rwork0.262 1220 -
obs--92.72 %

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