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- PDB-2cju: Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone ... -

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Basic information

Entry
Database: PDB / ID: 2cju
TitleCrystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ16- 113.8 scFv in complex with phOxGABA
Components(NQ16-113.8 ANTI-PHOX ANTIBODY) x 2
KeywordsIMMUNE SYSTEM / SCFV / ANTIBODY / IMMUNOGLOBULIN / 2-PHENYL-5-OXAZOLONE / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PHX / Ig heavy chain V region M603
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsScotti, C. / Gherardi, E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of Affinity Maturation of the Tepc15/V(Kappa)45.1 Anti-2-Phenyl-5-Oxazolone Antibodies.
Authors: Scotti, C. / Gherardi, E.
History
DepositionApr 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns_shell / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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
H: NQ16-113.8 ANTI-PHOX ANTIBODY
L: NQ16-113.8 ANTI-PHOX ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0893
Polymers25,8152
Non-polymers2741
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-18 kcal/mol
Surface area12880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)51.970, 74.190, 134.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11L-2003-

HOH

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Components

#1: Antibody NQ16-113.8 ANTI-PHOX ANTIBODY


Mass: 13390.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ16/113.8 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P01789*PLUS
#2: Antibody NQ16-113.8 ANTI-PHOX ANTIBODY


Mass: 12423.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ16/113.8 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115
#3: Chemical ChemComp-PHX / 4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID


Mass: 274.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1 M TRIS-HCL, PH 8.4, 0.2 M AMMONIUM SULPHATE, 37% PEG 8K, 6% SUCROSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2002 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17246 / % possible obs: 97.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.34 / % possible all: 89.3

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Processing

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

1flr


Resolution: 2.5→30 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1470440 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.291 433 5 %RANDOM
Rwork0.241 ---
obs0.241 9094 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.7 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 20 26 1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.74
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.438 40 4.9 %
Rwork0.322 811 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2GABA170603.PARAMGABA170603.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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