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- PDB-3qg7: Structural Basis for Ligand Recognition and Discrimination of a Q... -

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Basic information

Entry
Database: PDB / ID: 3qg7
TitleStructural Basis for Ligand Recognition and Discrimination of a Quorum Quenching Antibody
Components
  • AP4-24H11 Antibody Heavy Chain
  • AP4-24H11 Antibody Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin Fold / Antigen Recognition / AIP4 / Secreted
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsKirchdoerfer, R.K. / Kaufmann, G.F. / Janda, J.D. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for Ligand Recognition and Discrimination of a Quorum-quenching Antibody.
Authors: Kirchdoerfer, R.N. / Garner, A.L. / Flack, C.E. / Mee, J.M. / Horswill, A.R. / Janda, K.D. / Kaufmann, G.F. / Wilson, I.A.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: AP4-24H11 Antibody Heavy Chain
L: AP4-24H11 Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8126
Polymers46,9422
Non-polymers8704
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-38 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.182, 183.182, 42.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Antibody AP4-24H11 Antibody Heavy Chain


Mass: 23047.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody AP4-24H11 Antibody Light Chain


Mass: 23894.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 % PEG 4000, 0.2 M di-ammonium hydrogen phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR 300 CCD / Detector: CCD / Date: Apr 11, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.78→91.67 Å / Num. all: 13033 / Num. obs: 13033 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.7
Reflection shellResolution: 2.78→2.854 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.9 / Num. unique all: 840 / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 15C8

15c8


Resolution: 2.78→91.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 27.611 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24028 644 4.9 %RANDOM
Rwork0.19464 ---
obs0.19685 13033 97.21 %-
all-13033 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.21 Å20 Å2
2--0.41 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.78→91.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 28 51 3351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223382
X-RAY DIFFRACTIONr_bond_other_d0.0010.022272
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9534600
X-RAY DIFFRACTIONr_angle_other_deg1.4083.0035554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.85824.046131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0221513
X-RAY DIFFRACTIONr_chiral_restr0.0540.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3381.52112
X-RAY DIFFRACTIONr_mcbond_other0.0331.5852
X-RAY DIFFRACTIONr_mcangle_it0.63423447
X-RAY DIFFRACTIONr_scbond_it0.66331270
X-RAY DIFFRACTIONr_scangle_it1.1864.51153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.782→2.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 48 -
Rwork0.292 792 -
obs--83.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.52560.1682-0.73850.8256-0.91251.74570.0287-0.0253-0.0225-0.05720.1167-0.0447-0.0726-0.1547-0.1454-0.04440.02410.00040.03760.00180.015716.055253.43399.6372
23.37381.53771.91822.37280.93841.0931-0.05190.1397-0.57540.01830.187-0.1845-0.0540.2004-0.1351-0.1379-0.14710.00840.1220.00860.0506-1.221826.247212.2692
31.86950.40860.68431.22491.00111.1042-0.04090.1210.102-0.03970.01660.0648-0.0891-0.1810.0243-0.07410.07350.02440.13910.0493-0.0438-2.229760.0152-1.8044
40.89860.5648-0.10182.4225-1.8042.20840.1189-0.076-0.12550.129-0.2164-0.0907-0.1654-0.19680.0975-0.154-0.226-0.01320.18220.0665-0.0279-16.028131.369717.1968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 114
2X-RAY DIFFRACTION2H115 - 227
3X-RAY DIFFRACTION3L1 - 107
4X-RAY DIFFRACTION4L108 - 211

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