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- PDB-1a6w: B1-8 FV FRAGMENT COMPLEXED WITH A (4-HYDROXY-5-IODO-3-NITROPHENYL... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1a6w
TitleB1-8 FV FRAGMENT COMPLEXED WITH A (4-HYDROXY-5-IODO-3-NITROPHENYL) ACETATE COMPOUND
Components
  • B1-8 FV (HEAVY CHAIN)
  • B1-8 FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / HAPTEN
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response
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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-NIP / Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104 / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSimon, T. / Henrick, K. / Hirshberg, M. / Winter, G.
Citation
Journal: To be Published
Title: X-Ray Structures of Fv Fragment and its (4-Hydroxy-3-Nitrophenyl)Acetate Complex of Murine B1-8 Antibody
Authors: Simon, T. / Henrick, K. / Hirshberg, M. / Winter, G.
#1: Journal: Protein Eng. / Year: 1992
Title: A Functional Antibody Mutant with an Insertion in the Framework Region 3 Loop of the Vh Domain: Implications for Antibody Engineering
Authors: Simon, T. / Rajewsky, K.
History
DepositionMar 3, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: B1-8 FV (LIGHT CHAIN)
H: B1-8 FV (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3803
Polymers24,9452
Non-polymers4351
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-18 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.270, 83.510, 40.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody B1-8 FV (LIGHT CHAIN)


Mass: 11503.741 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: C57BL-6 / References: UniProt: P01724
#2: Antibody B1-8 FV (HEAVY CHAIN)


Mass: 13440.945 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: C57BL/6 / References: UniProt: P01751
#3: Chemical ChemComp-NIP / 4-HYDROXY-5-IODO-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID ANION


Mass: 435.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16IN2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.43 Å3/Da / Density % sol: 40.5 %
Crystal growMethod: dialysis
Details: THE PURIFIED PROTEIN HAS BEEN DIALYSED INTO A 10 MM TRIS-HCL PH 7.5 BUFFER ALSO CONTAINING 20 MM NACL. PEG 1550 WAS USED AS PRECIPITANT., dialysis

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Data collection

DiffractionMean temperature: 269 K
Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→36 Å / Num. obs: 65498 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.301 / % possible all: 79.2

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Processing

Software
NameClassification
MOSFLMdata reduction
AGROVATA/ROTAVATAdata reduction
MLPHAREphasing
PROLSQrefinement
Agrovatadata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.171 -
obs-15982
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 17 182 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.91.5
X-RAY DIFFRACTIONp_mcangle_it1.42
X-RAY DIFFRACTIONp_scbond_it1.52
X-RAY DIFFRACTIONp_scangle_it2.33
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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