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- PDB-2op4: Crystal Structure of Quorum-Quenching Antibody 1G9 -

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Basic information

Entry
Database: PDB / ID: 2op4
TitleCrystal Structure of Quorum-Quenching Antibody 1G9
Components
  • Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
  • Murine Antibody Fab RS2-1G9 Lambda Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / antibody / Fab / induced fit / quorum sensing / homoserine lactone
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKirchdoerfer, R.N. / Debler, E.W. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of a Quorum-quenching Antibody.
Authors: Debler, E.W. / Kaufmann, G.F. / Kirchdoerfer, R.N. / Mee, J.M. / Janda, K.D. / Wilson, I.A.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 999SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY SEQUENCE DATABASES. THE ...SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY SEQUENCE DATABASES. THE RESIDUE NUMBERING IN CHAINS L AND H FOLLOWS THE STANDARD KABAT NUMBERING SCHEME

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Murine Antibody Fab RS2-1G9 Lambda Light Chain
H: Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0563
Polymers46,9942
Non-polymers621
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-22 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.925, 72.041, 116.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe entry contains the crystallographic asymmetric unit which consists of 1 biological molecule: LH.

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Components

#1: Antibody Murine Antibody Fab RS2-1G9 Lambda Light Chain


Mass: 22911.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Purified from ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain


Mass: 24082.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Purified from ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: Q5BJZ2*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% (w/v) PEG 8000, 0.1M Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 11938 / Num. obs: 11938 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 83.5 Å2 / Rsym value: 0.062 / Net I/σ(I): 26.1
Reflection shellResolution: 2.85→2.924 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 782 / Rsym value: 0.534 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0017refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NTF

2ntf


Resolution: 2.85→35.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 39.254 / SU ML: 0.327 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26329 556 4.8 %RANDOM
Rwork0.19959 ---
all0.20255 11064 --
obs0.20255 11064 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.85→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 4 0 3281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223372
X-RAY DIFFRACTIONr_bond_other_d0.0020.022187
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9374614
X-RAY DIFFRACTIONr_angle_other_deg0.8373.0025354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12624.094127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42115506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1961510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02669
X-RAY DIFFRACTIONr_nbd_refined0.2270.2613
X-RAY DIFFRACTIONr_nbd_other0.2150.22187
X-RAY DIFFRACTIONr_nbtor_refined0.20.21653
X-RAY DIFFRACTIONr_nbtor_other0.0960.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.25
X-RAY DIFFRACTIONr_mcbond_it0.5271.52609
X-RAY DIFFRACTIONr_mcbond_other0.0791.5865
X-RAY DIFFRACTIONr_mcangle_it0.72123475
X-RAY DIFFRACTIONr_scbond_it1.0631506
X-RAY DIFFRACTIONr_scangle_it1.5994.51139
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.575 46 -
Rwork0.329 771 -
obs--99.88 %
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)
13.3467-1.54290.13635.8577-0.49653.6793-0.0552-0.4025-0.34810.06040.08990.41870.1718-0.1849-0.0347-0.23910.01170.08060.09260.1077-0.07740.41879.99815.9355
22.51170.2710.54113.17063.1687.3684-0.07950.0457-0.13880.43070.04940.34920.6115-0.28450.0302-0.15860.0461-0.0359-0.07270.0553-0.0235-7.606210.6013-15.0959
32.722-1.72251.12062.96490.53635.58280.1576-0.1933-0.54-0.30310.04690.24980.31-0.2704-0.2045-0.0534-0.0310.0185-0.04350.1456-0.097713.0932-5.27399.3845
44.8911-2.08010.81318.11810.58855.9276-0.08190.0740.15-0.2550.48470.1204-0.04830.4336-0.4027-0.180.0341-0.05730.0896-0.1929-0.21796.637710.8423-23.071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1071 - 110
2X-RAY DIFFRACTION2LA108 - 212111 - 212
3X-RAY DIFFRACTION3HB1 - 1131 - 122
4X-RAY DIFFRACTION4HB114 - 228123 - 222

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