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- PDB-1h8s: Three-dimensional structure of anti-ampicillin single chain Fv fr... -

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Basic information

Entry
Database: PDB / ID: 1h8s
TitleThree-dimensional structure of anti-ampicillin single chain Fv fragment complexed with the hapten.
ComponentsMUTANT AL2 6E7P9G
KeywordsANTI-AMPICILLIN ANTIBODIES
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-AIC
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsBurmester, J. / Spinelli, S. / Pugliese, L. / Krebber, A. / Honegger, A. / Jung, S. / Schimmele, B. / Cambillau, C. / Pluckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Selection, Characterization and X-Ray Structure of Anti-Ampicillin Single-Chain Fv Fragments from Phage-Displayed Murine Antibody Libraries
Authors: Burmester, J. / Spinelli, S. / Pugliese, L. / Krebber, A. / Honegger, A. / Jung, S. / Schimmele, B. / Cambillau, C. / Pluckthun, A.
History
DepositionFeb 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2001Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MUTANT AL2 6E7P9G
B: MUTANT AL2 6E7P9G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5555
Polymers54,0132
Non-polymers5423
Water5,350297
1
A: MUTANT AL2 6E7P9G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5484
Polymers27,0071
Non-polymers5423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MUTANT AL2 6E7P9G


Theoretical massNumber of molelcules
Total (without water)27,0071
Polymers27,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.930, 89.270, 94.410
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 MUTANT AL2 6E7P9G


Mass: 27006.734 Da / Num. of mol.: 2 / Fragment: FV FRAGMENT
Source method: isolated from a genetically manipulated source
Details: SINGLE CHAIN FV ANTIBODY IN WHICH THE VL AND VH FRAGMENTS ARE JOINED BY A GGGGSGGGGSGGGGSGGGGS LINKER
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PAK3000 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): RV308
#2: Chemical ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID


Mass: 349.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O4S / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 46.49 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.85 mg/mlprotein1drop
21.9-2.0 Mammonium sulfate1reservoir
3100 mMsodium acetate1reservoirpH5.8
433 mMampicillin1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→13 Å / Num. obs: 20445 / % possible obs: 98 % / Redundancy: 3 % / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.082 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.2 / % possible all: 92
Reflection
*PLUS
% possible obs: 98 % / Num. measured all: 93952 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 82.8 % / Rmerge(I) obs: 0.225

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.4→12.94 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1287 6.7 %RANDOM
Rwork0.204 ---
obs0.204 19137 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.6877 Å2 / ksol: 0.335775 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→12.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 34 297 3731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 214 7.4 %
Rwork0.292 2687 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2AMPI_231199.PARAMAMPI_300799.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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