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

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Basic information

Entry
Database: PDB / ID: 1cfv
TitleMONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI
Components(MONOCLONAL ANTIBODY FV4155) x 2
KeywordsIMMUNOGLOBULIN / FV FRAGMENT / STEROID HORMONE / FINE SPECIFICITY
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / immunoglobulin complex / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / adaptive immune response ...positive regulation of B cell activation / phagocytosis, recognition / immunoglobulin complex / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / adaptive immune response / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / extracellular space
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
ESTRONE BETA-D-GLUCURONIDE / Ig kappa chain V-II region 26-10 / Ig heavy chain V region RF
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
DepositionApr 11, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 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_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_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_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: MONOCLONAL ANTIBODY FV4155
H: MONOCLONAL ANTIBODY FV4155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2726
Polymers25,6302
Non-polymers6434
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-48 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.000, 90.000, 59.600
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-203-

HOH

21L-204-

HOH

31L-293-

HOH

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Components

#1: Antibody MONOCLONAL ANTIBODY FV4155 / FV4155


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


Mass: 13191.760 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P18524*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-E3G / ESTRONE BETA-D-GLUCURONIDE


Mass: 446.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.0
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-6 mg/mlprotein1drop
20.2 MZn acetate1drop
30.1 Msodium cacodylate1drop
418 %(w/v)PEG80001drop
50.2 MZn 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: Jan 1, 1996 / Details: MSC/YALE 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: 14295 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Rsym value: 0.064 / Net I/σ(I): 9.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.268 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 105121 / Rmerge(I) obs: 0.077

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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: OTHER REFINEMENT REMARKS: CONTACTS INVOLVING ZINC ATOMS CAN BE AT DISTANCES LESS THAN THE SPECIFIED DISTANCE CUTOFF OF 2.2 ANGSTROMS FOR CONTACTS NOT NOT INVOLVING HYDROGEN ATOMS. THE ...Details: OTHER REFINEMENT REMARKS: CONTACTS INVOLVING ZINC ATOMS CAN BE AT DISTANCES LESS THAN THE SPECIFIED DISTANCE CUTOFF OF 2.2 ANGSTROMS FOR CONTACTS NOT NOT INVOLVING HYDROGEN ATOMS. THE FOLLOWING ATOMS ARE SITUATED ACROSS A TWO-FOLD AXIS AND HAVE AN OCCUPANCY OF 0.5. IT IS THEREFORE POSSIBLE THAT THESE ATOMS ARE IN CLOSE CONTACT WITH OTHER ATOMS AT DISTANCES LESS THAN THOSE NORMALLY OBSERVED. ATM1 RES C SSEQI ZN ZN L 201 O HOH L 300 O HOH L 303 O HOH L 389 RESIDUE VAL L 56 HAS DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE IN THE GAMMA QUADRANT OF THE RAMACHANDRAN PLOT. SOLVENT MOLECULES HOH L 300, HOH L 301 AND HOH L 394 ARE SITUATED ON SPECIAL POSITIONS AND HAVE OCCUPANCIES OF 0.50. RESIDUE VAL L 56 HAS DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE IN THE GAMMA QUADRANT OF THE RAMACHANDRAN PLOT.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 658 5 %RANDOM
Rwork0.178 ---
all-13154 --
obs-12496 93.6 %-
Displacement parametersBiso mean: 19.76 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 34 198 2032
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_it1.3462
X-RAY DIFFRACTIONp_mcangle_it2.0972.5
X-RAY DIFFRACTIONp_scbond_it4.9945
X-RAY DIFFRACTIONp_scangle_it6.6926
X-RAY DIFFRACTIONp_plane_restr0.012
X-RAY DIFFRACTIONp_chiral_restr0.10.12
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.1940.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_tor5.27920
X-RAY DIFFRACTIONp_staggered_tor16.27520
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.01920
X-RAY DIFFRACTIONp_special_tor020
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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