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- PDB-2c1p: Fab-fragment of enantioselective antibody complexed with finrozole -

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Basic information

Entry
Database: PDB / ID: 2c1p
TitleFab-fragment of enantioselective antibody complexed with finrozole
Components
  • IGH-4 PROTEIN
  • IGK-C PROTEIN
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ENANTIOSELECTIVE / FINROZOLE / ANTIBODY / ENANTIOSELECTIVE ANTIBODY / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


immune response / extracellular space / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-FNZ / Igk protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsParkkinen, T. / Nevanen, T.K. / Koivula, A. / Rouvinen, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of an Enantioselective Fab-Fragment in Free and Complex Forms.
Authors: Parkkinen, T. / Nevanen, T.K. / Koivula, A. / Rouvinen, J.
History
DepositionSep 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 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 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGK-C PROTEIN
B: IGH-4 PROTEIN
H: IGH-4 PROTEIN
L: IGK-C PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4326
Polymers94,7884
Non-polymers6452
Water7,728429
1
A: IGK-C PROTEIN
B: IGH-4 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7163
Polymers47,3942
Non-polymers3221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: IGH-4 PROTEIN
L: IGK-C PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7163
Polymers47,3942
Non-polymers3221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.815, 87.419, 141.684
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 IGK-C PROTEIN / FINROZOLE-BINDING ANTIBODY


Mass: 24027.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RV308 / References: UniProt: Q58EU8*PLUS
#2: Antibody IGH-4 PROTEIN / FINROZOLE-BINDING ANTIBODY


Mass: 23366.123 Da / Num. of mol.: 2 / Fragment: FAB-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): RV308
#3: Chemical ChemComp-FNZ / 4-[(1S,2R)-3-(4-FLUOROPHENYL)-2-HYDROXY-1-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]BENZONITRILE


Mass: 322.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15FN4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.5 / Details: 22% PEG3350,0.1 M TRIS,10 EXCESS LIGAND, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8122
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8122 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 171606 / % possible obs: 78.3 % / Observed criterion σ(I): 7.1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4 / % possible all: 68.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F8T

1f8t


Resolution: 2→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 4394 7.3 %RANDOM
Rwork0.2302 ---
obs0.2302 43683 72.6 %-
Solvent computationBsol: 44.3408 Å2 / ksol: 0.348283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.068 Å20 Å20 Å2
2--0.274 Å20 Å2
3---9.794 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 48 429 7101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006039
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_deg1.39654
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5FINROZOLE.PARFINROZOLE.TOP

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