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- PDB-1q0x: Anti-morphine Antibody 9B1 Unliganded Form -

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Basic information

Entry
Database: PDB / ID: 1q0x
TitleAnti-morphine Antibody 9B1 Unliganded Form
Components
  • Fab 9B1, heavy chain
  • Fab 9B1, light chain
KeywordsIMMUNE SYSTEM / ANTI-MORPHINE ANTIBODY / FAB FRAGMENT
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig lambda-1 chain V region / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPozharski, E. / Wilson, M.A. / Hewagama, A. / Shanafelt, A.B. / Petsko, G. / Ringe, D.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Anchoring a cationic ligand: the structure of the Fab fragment of the anti-morphine antibody 9B1 and its complex with morphine
Authors: Pozharski, E. / Wilson, M.A. / Hewagama, A. / Shanafelt, A.B. / Petsko, G. / Ringe, D.
History
DepositionJul 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999AUTHOR STATES NO DBREF AVAILABLE The author has stated that a database reference sequence is ...AUTHOR STATES NO DBREF AVAILABLE The author has stated that a database reference sequence is unavailable for either chain in this structure.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 9B1, light chain
H: Fab 9B1, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6705
Polymers46,2842
Non-polymers3863
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-40 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.514, 59.924, 114.706
Angle α, β, γ (deg.)90.00, 92.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-412-

HOH

21H-603-

HOH

31H-659-

HOH

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Components

#1: Antibody Fab 9B1, light chain


Mass: 22525.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01723
#2: Antibody Fab 9B1, heavy chain


Mass: 23758.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: Q9D9B8*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 22% PEG MME 2000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 4.60

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001
RadiationMonochromator: BENT CONICAL SI-MIRROR (RH COATING) + BENT GE(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 50732 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.63 % / Mean I/σ(I) obs: 1.52 / % possible all: 97.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 15C8 (CONSTANT DOMAIN) + PDB ENTRY 1E4X (VARIABLE DOMAIN)

15c8

1e4x


Resolution: 1.6→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: BULK SOLVENT MASK CORRECTED TO EXCLUDE INTERNAL CAVITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2540 4.9 %RANDOM
Rwork0.216 ---
obs0.216 50732 98.5 %-
all-50732 --
Solvent computationBsol: 37.09 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.803 Å20 Å23.483 Å2
2--1.85 Å20 Å2
3----0.047 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 23 327 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it2.792
X-RAY DIFFRACTIONc_scangle_it3.852.5
LS refinement shellResolution: 1.6→1.65 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.349 244 4.77 %
Rwork0.323 4308 -
obs--88.9 %

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