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- PDB-1kfa: Crystal structure of Fab fragment complexed with gibberellin A4 -

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Basic information

Entry
Database: PDB / ID: 1kfa
TitleCrystal structure of Fab fragment complexed with gibberellin A4
Components
  • monoclonal antibody heavy chain
  • monoclonal antibody light chain
KeywordsIMMUNE SYSTEM / Immunoglobuiln fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / GIBBERELLIN A4
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMurata, T. / Fushinobu, S. / Nakajima, M. / Asami, O. / Sassa, T. / Wakagi, T. / Yamaguchi, I.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment.
Authors: Murata, T. / Fushinobu, S. / Nakajima, M. / Asami, O. / Sassa, T. / Wakagi, T. / Yamaguchi, I.
#1: Journal: PLANT CELL.PHYSIOL. / Year: 1991
Title: Monoclonal antibodies specific for non-derivatized gibberellins I
Authors: Nakajima, M. / Yamaguchi, I. / Nagatani, A. / Kizawa, S. / Murofushi, N. / Furuya, N. / Takahashi, N.
History
DepositionNov 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2013Group: Source and taxonomy
Revision 1.4Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: 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: monoclonal antibody light chain
H: monoclonal antibody heavy chain
M: monoclonal antibody light chain
I: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6956
Polymers95,0304
Non-polymers6652
Water2,126118
1
L: monoclonal antibody light chain
H: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8483
Polymers47,5152
Non-polymers3321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-28 kcal/mol
Surface area18950 Å2
MethodPISA
2
M: monoclonal antibody light chain
I: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8483
Polymers47,5152
Non-polymers3321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-27 kcal/mol
Surface area18540 Å2
MethodPISA
3
L: monoclonal antibody light chain
H: monoclonal antibody heavy chain
hetero molecules

M: monoclonal antibody light chain
I: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6956
Polymers95,0304
Non-polymers6652
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area9590 Å2
ΔGint-62 kcal/mol
Surface area35910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.076, 150.146, 106.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody monoclonal antibody light chain


Mass: 23754.285 Da / Num. of mol.: 2 / Fragment: residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo / Cell (production host): Hybridoma cell / Cellular location (production host): ascitic fluid / Production host: Mus musculus (house mouse)
#2: Antibody monoclonal antibody heavy chain


Mass: 23760.887 Da / Num. of mol.: 2 / Fragment: Variable domain, constant domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo / Cell (production host): Hybridoma cell / Cellular location (production host): ascitic fluid / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-GA4 / GIBBERELLIN A4


Mass: 332.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(v/v)glycerol1reservoir
212 %(w/v)PEG33501reservoir
30.06 MBis-Tris-HCl1reservoirpH6.5
48 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→39.62 Å / Num. all: 402565 / Num. obs: 402565 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3799 / Rsym value: 0.321 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 26460 / % possible obs: 100 % / Num. measured all: 402565
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ikf

1ikf


Resolution: 2.8→39.62 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1685086.35 / Data cutoff low absF: 0 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1192 5 %random
Rwork0.235 ---
all0.243 26440 --
obs0.261 23741 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0048 Å2 / ksol: 0.373888 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.94 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 48 118 6677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 194 5 %
Rwork0.242 --
obs-3709 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ga4.paramga4.top
Refinement
*PLUS
Highest resolution: 2.8 Å / Num. reflection obs: 22549 / % reflection Rfree: 5 % / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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