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- PDB-2bfv: MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 2bfv
TitleMONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI
Components(FV4155) x 2
KeywordsIMMUNOGLOBULIN / FV FRAGMENT / STEROID HORMONE / FINE SPECIFICITY
Function / homology
Function and homology information


immunoglobulin complex / antigen binding / 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
ESTRIOL 3-(B-D-GLUCURONIDE) / Ig kappa chain V-II region 26-10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTrinh, C.H. / Phillips, S.E.V.
CitationJournal: Structure / Year: 1997
Title: Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity.
Authors: Trinh, C.H. / Hemmington, S.D. / Verhoeyen, M.E. / Phillips, S.E.
History
DepositionMay 27, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FV4155
H: FV4155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0943
Polymers25,6302
Non-polymers4651
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-22 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.600, 53.600, 83.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody FV4155


Mass: 12437.998 Da / Num. of mol.: 1 / Fragment: MONOCLONAL ANTIBODY FV FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P01631
#2: Antibody FV4155


Mass: 13191.760 Da / Num. of mol.: 1 / Fragment: MONOCLONAL ANTIBODY FV FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
#3: Chemical ChemComp-STG / ESTRIOL 3-(B-D-GLUCURONIDE)


Mass: 464.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 15% (W/V) PEG 4000, 100MM NA ACETATE AND 50MM TRIS HCL PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-3 mg/mlprotein1drop
20.05 MNa acetate1drop
30.025 MTris-HCl1drop
47.5 %(w/v)PEG40001drop
50.1 MNa acetate1reservoir
60.05 MTris-HCl1reservoir
715 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: MSC DOUBLE FOCUSING MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 7836 / % possible obs: 86.9 % / Observed criterion σ(I): 3 / Redundancy: 1.5 % / Rsym value: 0.064 / Net I/σ(I): 7.21
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.225 / % possible all: 87.5
Reflection
*PLUS
Num. measured all: 12233 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 87.5 % / Rmerge(I) obs: 0.225

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
PROLSQrefinement
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBV

1nbv


Resolution: 2.5→10 Å / σ(F): 0
Details: VAL L 56 HAS DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE IN THE GAMMA QUADRANT OF THE RAMACHANDRAN PLOT.
RfactorNum. reflection% reflection
Rwork0.187 --
all-7740 -
obs-7740 84 %
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 33 55 1877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord00.05
X-RAY DIFFRACTIONp_mcbond_it1.1992
X-RAY DIFFRACTIONp_mcangle_it2.0542.5
X-RAY DIFFRACTIONp_scbond_it5.6066
X-RAY DIFFRACTIONp_scangle_it8.057
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2140.3
X-RAY DIFFRACTIONp_planar_tor4.25920
X-RAY DIFFRACTIONp_staggered_tor17.55920
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.08320
X-RAY DIFFRACTIONp_special_tor020
Software
*PLUS
Name: PROLSQ(CCP4) / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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