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- PDB-1xgy: Crystal Structure of Anti-Meta I Rhodopsin Fab Fragment K42-41L -

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Basic information

Entry
Database: PDB / ID: 1xgy
TitleCrystal Structure of Anti-Meta I Rhodopsin Fab Fragment K42-41L
Components
  • K42-41L Fab Heavy Chain
  • K42-41L Fab Light Chain
  • Rhodopsin Epitope Mimetic Peptide
KeywordsIMMUNE SYSTEM / Meta-I / Rhodopsin / Fab / Igg / K42-41L / Phage display / antibody / immunoglobulin / antibody imprinting / peptide mimetics
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 / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsPiscitelli, C.L. / Angel, T.E. / Bailey, B.W. / Lawerence, C.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Equilibrium between metarhodopsin-I and metarhodopsin-II is dependent on the conformation of the third cytoplasmic loop.
Authors: Piscitelli, C.L. / Angel, T.E. / Bailey, B.W. / Hargrave, P. / Dratz, E.A. / Lawrence, C.M.
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE Suitable sequence database reference not available

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: K42-41L Fab Light Chain
H: K42-41L Fab Heavy Chain
M: K42-41L Fab Light Chain
I: K42-41L Fab Heavy Chain
P: Rhodopsin Epitope Mimetic Peptide
Q: Rhodopsin Epitope Mimetic Peptide


Theoretical massNumber of molelcules
Total (without water)96,8866
Polymers96,8866
Non-polymers00
Water1,35175
1
L: K42-41L Fab Light Chain
H: K42-41L Fab Heavy Chain
P: Rhodopsin Epitope Mimetic Peptide


Theoretical massNumber of molelcules
Total (without water)48,4433
Polymers48,4433
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: K42-41L Fab Light Chain
I: K42-41L Fab Heavy Chain
Q: Rhodopsin Epitope Mimetic Peptide


Theoretical massNumber of molelcules
Total (without water)48,4433
Polymers48,4433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-25 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.721, 196.646, 44.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-216-

HOH

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Components

#1: Antibody K42-41L Fab Light Chain


Mass: 23807.518 Da / Num. of mol.: 2 / Fragment: Anitgen Binding Fragment, Fab / Source method: isolated from a natural source
Details: SP2/0 mouse myeloma cells fused with immunized mouse splenocytes
Source: (natural) Mus musculus (house mouse)
#2: Antibody K42-41L Fab Heavy Chain


Mass: 23644.568 Da / Num. of mol.: 2 / Fragment: Antigen Binding Fragment, Fab / Source method: isolated from a natural source
Details: SP2/0 mouse myeloma cells fused with immunized mouse splenocytes
Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6PF95
#3: Protein/peptide Rhodopsin Epitope Mimetic Peptide


Mass: 991.100 Da / Num. of mol.: 2 / Fragment: Phage Display Consensus Peptide / Source method: obtained synthetically / Details: Chemically synthesized.
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: peg mme 5000, MES, Ammonium Sulfate, Peptide TGALQERSK, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 28, 2003 / Details: OSMIC BLUE
RadiationMonochromator: NI MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.71→98.32 Å / Num. all: 21152 / Num. obs: 21152 / % possible obs: 78.2 % / Observed criterion σ(F): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 41.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 12.7
Reflection shellResolution: 2.71→2.83 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1122 / % possible all: 43.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1N6Q, 1FAI

1n6q

1fai


Resolution: 2.71→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1635857.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1070 5.1 %RANDOM
Rwork0.233 ---
all0.276 21049 --
obs0.233 21049 78.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.9482 Å2 / ksol: 0.323055 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2---7.49 Å20 Å2
3---5.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.71→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 0 75 6778
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.9
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.71→2.83 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.461 73 5.3 %
Rwork0.402 1778 -
obs-1432 43.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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