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

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Basic information

Entry
Database: PDB / ID: 2uud
TitleCrystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ10- 1.12 scFv in complex with the hapten
Components(NQ10-1.12 ANTI-PHOX ANTIBODY) x 3
KeywordsIMMUNE SYSTEM / SCFV / ANTIBODY / IMMUNOGLOBULIN / 2-PHENYL-5-OXAZOLONE / IMMUNOGLOBULIN DOMAIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-PHX
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsScotti, C. / Gherardi, E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of Affinity Maturation of the Tepc15-Vkappa45.1 Anti-2-Phenyl-5-Oxazolone Antibodies
Authors: Scotti, C. / Gherardi, E.
History
DepositionMar 2, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionApr 3, 2007ID: 2CJV
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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.pdbx_leaving_atom_flag / _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.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
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
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

Downloads & links

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Assembly

Deposited unit
H: NQ10-1.12 ANTI-PHOX ANTIBODY
J: NQ10-1.12 ANTI-PHOX ANTIBODY
K: NQ10-1.12 ANTI-PHOX ANTIBODY
L: NQ10-1.12 ANTI-PHOX ANTIBODY
S: NQ10-1.12 ANTI-PHOX ANTIBODY
T: NQ10-1.12 ANTI-PHOX ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7858
Polymers54,2366
Non-polymers5492
Water91951
1
H: NQ10-1.12 ANTI-PHOX ANTIBODY
L: NQ10-1.12 ANTI-PHOX ANTIBODY
S: NQ10-1.12 ANTI-PHOX ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3924
Polymers27,1183
Non-polymers2741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
J: NQ10-1.12 ANTI-PHOX ANTIBODY
K: NQ10-1.12 ANTI-PHOX ANTIBODY
T: NQ10-1.12 ANTI-PHOX ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3924
Polymers27,1183
Non-polymers2741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.944, 75.657, 52.854
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.79791, -0.03704, 0.60164), (-0.04153, -0.99912, -0.00643), (0.60135, -0.01985, -0.79874)7.65293, 37.41358, -20.95366
2given(0.79791, -0.03704, 0.60164), (-0.04153, -0.99912, -0.00643), (0.60135, -0.01985, -0.79874)7.65293, 37.41358, -20.95366
3given(0.79791, -0.03704, 0.60164), (-0.04153, -0.99912, -0.00643), (0.60135, -0.01985, -0.79874)7.65293, 37.41358, -20.95366

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Components

#1: Antibody NQ10-1.12 ANTI-PHOX ANTIBODY


Mass: 13410.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115
#2: Antibody NQ10-1.12 ANTI-PHOX ANTIBODY


Mass: 12423.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115
#3: Antibody NQ10-1.12 ANTI-PHOX ANTIBODY


Mass: 1283.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115
#4: 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.: 2 / Source method: obtained synthetically / Formula: C14H14N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.45 Å3/Da / Density % sol: 49.32 %
Crystal growpH: 7.6
Details: 0.1 M TRIS-HCL, PH 7.6, 0.2 M AMMONIUM SULPHATE, 30% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2002 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→65.64 Å / Num. obs: 11988 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 75.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.22 / % possible all: 99.1

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Processing

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

1flr


Resolution: 2.9→19.9 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 809326.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FOR REFINEMENT-REBUILDING, THE PROGRAM LAFIRE HAS BEEN USED, STARTING FROM THE 2CJV STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.297 574 5 %RANDOM
Rwork0.228 ---
obs0.228 11404 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3383 Å2 / ksol: 0.336356 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 40 51 3833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
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: 2.9→2.99 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.419 60 5.8 %
Rwork0.157 1026 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GABA.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION5GABA.PARAMGABA.TOP

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