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- PDB-1bfv: MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1bfv
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 / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular region
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 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 / Ig heavy chain V region 5-76
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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

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Assembly

Deposited unit
L: FV4155
H: FV4155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2906
Polymers25,6302
Non-polymers6614
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-61 kcal/mol
Surface area10530 Å2
MethodPISA
2
L: FV4155
H: FV4155
hetero molecules

L: FV4155
H: FV4155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,58112
Polymers51,2604
Non-polymers1,3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area8010 Å2
ΔGint-335 kcal/mol
Surface area18550 Å2
MethodPISA
3
H: FV4155
hetero molecules

H: FV4155
hetero molecules

L: FV4155
hetero molecules

L: FV4155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,58112
Polymers51,2604
Non-polymers1,3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area3770 Å2
ΔGint-149 kcal/mol
Surface area22600 Å2
MethodPISA
4
H: FV4155
hetero molecules

L: FV4155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2906
Polymers25,6302
Non-polymers6614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area1600 Å2
ΔGint-71 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.900, 89.900, 59.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11L-202-

HOH

21L-205-

HOH

31L-286-

HOH

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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 / References: UniProt: P18529*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-STG / ESTRIOL 3-(B-D-GLUCURONIDE)


Mass: 464.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O9
#5: 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-3 mg/mlprotein1drop
20.1 Mzinc acetate1drop
30.05 Msodium cacodylate1drop
49 %(w/v)PEG80001drop
50.2 Mzinc acetate1reservoir
60.1 Msodium cacodylate1reservoir
718 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1996 / 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: 2.1→20 Å / Num. obs: 14834 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 8.8 % / Rsym value: 0.074 / Net I/σ(I): 9.53
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.243 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 129898 / Rmerge(I) obs: 0.074

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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: 2.1→10 Å / Cross valid method: THROUGHOUT / 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% reflectionSelection details
Rfree0.271 724 5 %RANDOM
Rwork0.187 ---
all-14473 --
obs-13749 98.42 %-
Displacement parametersBiso mean: 21.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 36 182 2012
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_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord00.05
X-RAY DIFFRACTIONp_mcbond_it1.5622
X-RAY DIFFRACTIONp_mcangle_it2.4352.5
X-RAY DIFFRACTIONp_scbond_it5.7895
X-RAY DIFFRACTIONp_scangle_it7.8726
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1090.12
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.1930.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1750.3
X-RAY DIFFRACTIONp_planar_tor3.87920
X-RAY DIFFRACTIONp_staggered_tor14.64720
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.00820
X-RAY DIFFRACTIONp_special_tor020
Software
*PLUS
Name: 'PROLSQ (CCP4)' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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