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- PDB-2c1o: ENAIIHis Fab fragment in the free form -

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Basic information

Entry
Database: PDB / ID: 2c1o
TitleENAIIHis Fab fragment in the free form
Components
  • IGH-4 PROTEIN
  • IGK-C PROTEIN
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ENANTIOSELECTIVE / FINROZOLE / ANTIBODY / ENA11HIS ANTIBODY / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,1734
Polymers103,1734
Non-polymers00
Water3,459192
1
A: IGK-C PROTEIN
B: IGH-4 PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,5872
Polymers51,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: IGH-4 PROTEIN
L: IGK-C PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,5872
Polymers51,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.805, 88.680, 141.441
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 / ENA11HIS ANTIBODY


Mass: 28091.432 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 / ENA11HIS ANTIBODY


Mass: 23495.236 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 7.5 / Details: 20 % PEG3350, 0.1 M HEPES, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8122
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8122 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 23952 / % possible obs: 95.6 % / Observed criterion σ(I): 3.2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.4 / % possible all: 83.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F8T

1f8t


Resolution: 2.75→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3011 2287 9.5 %RANDOM
Rwork0.2184 ---
obs0.2184 23179 95.9 %-
Solvent computationBsol: 24.0959 Å2 / ksol: 0.291701 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.774 Å20 Å20 Å2
2---10.902 Å20 Å2
3---13.676 Å2
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 0 192 6848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007458
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_deg1.45616
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 DIFFRACTION5LISA.TOP

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