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- PDB-1dzb: Crystal structure of phage library-derived single-chain Fv fragme... -

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Basic information

Entry
Database: PDB / ID: 1dzb
TitleCrystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme
Components
  • SCFV FRAGMENT 1F9
  • TURKEY EGG-WHITE LYSOZYME C
KeywordsIMMUNE SYSTEM / COMPLEX (ANTIBODY ANTIGEN) / SINGLE-DOMAIN ANTIBODY / TURKEY EGG-WHITE LYSOZYME / ANTIBODY- PROTEIN COMPLEX / SINGLE-CHAIN FV FRAGMENT
Function / homology
Function and homology information


glycosaminoglycan binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAy, J. / Keitel, T. / Kuettner, G. / Wessner, H. / Scholz, C. / Hahn, M. / Hoehne, W.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of a Phage Library-Derived Single-Chain Fv Fragment Complexed with Turkey Egg -White Lysozyme at 2.0 A Resolution
Authors: Ay, J. / Keitel, T. / Kuttner, G. / Wessner, H. / Scholz, C. / Hahn, M. / Hohne, W.
#1: Journal: Mol.Immunol. / Year: 1998
Title: A Phage Library-Derived Single-Chain Fv Fragment in Complex with a Phage Library-Derived Single-Chain Fv Fragment in Complex Withturkey Egg-White Lysozyme: Characterization, Crystallization ...Title: A Phage Library-Derived Single-Chain Fv Fragment in Complex with a Phage Library-Derived Single-Chain Fv Fragment in Complex Withturkey Egg-White Lysozyme: Characterization, Crystallization Andpreliminary X-Ray Analysis
Authors: Kuttner, G. / Keitel, T. / Giessmann, E. / Wessner, H. / Scholz, C.
History
DepositionFeb 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: SCFV FRAGMENT 1F9
B: SCFV FRAGMENT 1F9
X: TURKEY EGG-WHITE LYSOZYME C
Y: TURKEY EGG-WHITE LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)82,9644
Polymers82,9644
Non-polymers00
Water4,684260
1
A: SCFV FRAGMENT 1F9
X: TURKEY EGG-WHITE LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)41,4822
Polymers41,4822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SCFV FRAGMENT 1F9
Y: TURKEY EGG-WHITE LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)41,4822
Polymers41,4822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.710, 112.440, 80.000
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody SCFV FRAGMENT 1F9


Mass: 27253.922 Da / Num. of mol.: 2 / Fragment: SEE REMARK 400 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / References: TrEMBL: CAA05093, TrEMBL: CAA05094
#2: Protein TURKEY EGG-WHITE LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C


Mass: 14228.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MELEAGRIS GALLOPAVO (turkey) / References: UniProt: P00703, lysozyme
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A,B: EACH CHAIN IS MADE UP FROM: RESIDUES 1-116: HEAVY CHAIN VARIABLE REGION OF 1F9 RESIDUES ...CHAIN A,B: EACH CHAIN IS MADE UP FROM: RESIDUES 1-116: HEAVY CHAIN VARIABLE REGION OF 1F9 RESIDUES 117-131: GGGGSGGGGSGGGGS LINKER RESIDUES 201-307: LIGHT CHAIN VARIABLE REGION OF 1F9 RESIDUES 308-311: RAAA LINKER TO MYC TAG RESIDUES 312-322: EQKLISEEDLN MYC TAG THERE IS NO ELECTRON DENSITY FOUND FOR THE LINKERPEPTIDE (GGGGS)3 BETWEEN THE HEAVY CHAIN VARIABLE REGION AND THE LIGHT CHAIN VARIABLE REGION OF THE SCFV FRAGMENT. NO ELECTRON DENSITY WAS OBSERVED FOR THE LAST RESIDUE OF C-TERMINUS OF VL LYS-107 AND FOR THE FOUR RESIDUES (ARG-(ALA)3) CONNECTING THE C-TERMINUS OF VL AND THE MYC-TAG. FOR THE MYC-TAG IS ALSO NO ELECTRON DENSITY VISIBLE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 35.6 %
Description: THERE ARE TWO MOLECULE COMPLEXES PER ASYMMETRIC UNIT
Crystal growpH: 5
Details: A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND ...Details: A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000
Crystal
*PLUS
Density % sol: 55.3 %
Crystal grow
*PLUS
Method: vapor diffusion / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
25 mMTris-HCl1droppH7.5
30.05 Msodium acetate1droppH5.0
410 %(w/v)PEG40001drop
50.1 M1dropNaCl
60.1 Mammonium acetate1drop
730 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.045
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 40240 / % possible obs: 87.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.683 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.77 / % possible all: 75.5
Reflection
*PLUS
Num. measured all: 297921
Reflection shell
*PLUS
% possible obs: 75.5 % / Num. unique obs: 3449

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JHL

1jhl


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THERE ARE TWO MOLECULES PER ASYMMETRIC UNIT
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2011 5 %RANDOM
Rwork0.225 ---
obs-40205 87.9 %-
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 0 260 5702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0830.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7192.5
X-RAY DIFFRACTIONp_mcangle_it4.0254
X-RAY DIFFRACTIONp_scbond_it2.9232.5
X-RAY DIFFRACTIONp_scangle_it4.2094
X-RAY DIFFRACTIONp_plane_restr10.67
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1650.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor10.67
X-RAY DIFFRACTIONp_staggered_tor21.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.120
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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