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- PDB-2ntf: Crystal Structure of a Quorum-Quenching Antibody in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 2ntf
TitleCrystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog
Components
  • Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
  • Murine Antibody Fab RS2-1G9 Lambda Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / antibody / Fab / hapten complex / 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 / metal ion binding
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
3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE / : / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsDebler, 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
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT AVAILABLE IN ANY SEQUENCE DATABASES. THE ... SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT 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

Downloads & links

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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
A: Murine Antibody Fab RS2-1G9 Lambda Light Chain
B: Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4396
Polymers93,8464
Non-polymers5932
Water00
1
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)47,2203
Polymers46,9232
Non-polymers2961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-26 kcal/mol
Surface area20480 Å2
MethodPISA
2
A: Murine Antibody Fab RS2-1G9 Lambda Light Chain
B: Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2203
Polymers46,9232
Non-polymers2961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-27 kcal/mol
Surface area20410 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-48 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.659, 118.659, 176.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12L
22A
13H
23B
14H
24B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNVALVALLA1 - 1061 - 108
21GLNGLNVALVALAC1 - 1061 - 108
12GLYGLYARGARGLA107 - 211110 - 211
22GLYGLYARGARGAC107 - 211110 - 211
13GLNGLNSERSERHB1 - 1121 - 121
23GLNGLNSERSERBD1 - 1121 - 121
14ALAALAARGARGHB113 - 228122 - 222
24ALAALAARGARGBD113 - 228122 - 222

NCS ensembles :
ID
1
2
3
4
DetailsThe entry contains the crystallographic asymmetric unit which consists of 2 biological molecules: LH, AB.

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Components

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


Mass: 22840.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Purified from ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: Q0VDX6
#2: Antibody Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain


Mass: 24082.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Purified from ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: Q99LC4
#3: Chemical ChemComp-OHM / 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE


Mass: 296.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H28N2O3

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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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 298 K / pH: 8
Details: 1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 19140 / % possible obs: 88.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 77.3 Å2 / Rsym value: 0.096 / Net I/σ(I): 14.2
Reflection shellResolution: 3.18→3.25 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.508 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1A6V, 1MFB

1a6v

1mfb


Resolution: 3.18→44.02 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.881 / SU B: 50.456 / SU ML: 0.378 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 992 5.1 %RANDOM
Rwork0.21 ---
obs0.213 18458 89.1 %-
all-18770 --
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: 63.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 3.18→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 42 0 6652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226840
X-RAY DIFFRACTIONr_bond_other_d0.0040.024450
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9399360
X-RAY DIFFRACTIONr_angle_other_deg0.8943.00510826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2675862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95524.186258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.045151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9751520
X-RAY DIFFRACTIONr_chiral_restr0.0770.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021352
X-RAY DIFFRACTIONr_nbd_refined0.230.21463
X-RAY DIFFRACTIONr_nbd_other0.210.24521
X-RAY DIFFRACTIONr_nbtor_refined0.1990.23366
X-RAY DIFFRACTIONr_nbtor_other0.0960.23960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4140.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3310.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9271.55308
X-RAY DIFFRACTIONr_mcbond_other0.1351.51746
X-RAY DIFFRACTIONr_mcangle_it1.10727018
X-RAY DIFFRACTIONr_scbond_it1.66233073
X-RAY DIFFRACTIONr_scangle_it2.2964.52342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11L1361tight positional0.040.05
21A1309tight positional0.030.05
32H1610tight positional0.030.05
42B1225tight positional0.030.05
11L1361tight thermal0.120.5
21A1309tight thermal0.070.5
32H1610tight thermal0.060.5
42B1225tight thermal0.420.5
LS refinement shellResolution: 3.18→3.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 89 -
Rwork0.302 1425 -
obs--95.52 %
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)
13.2492-0.50390.95084.6544-0.05713.2205-0.25360.0115-0.2720.22150.15010.23660.15030.20190.1035-0.21310.08540.0086-0.2821-0.0296-0.2734-42.3084-2.47541.2798
23.3383-0.78840.95525.6764-0.40610.2891-0.23-0.12910.04520.0001-0.38310.37130.51230.67160.6131-0.28890.04720.346-0.4080.072-0.2127-38.877-26.608921.1051
36.4504-2.45462.57884.4486-2.26495.8687-0.40020.42760.3795-0.0813-0.1389-0.7063-0.0190.70530.5391-0.25310.02480.0211-0.07290.0716-0.0812-21.4597-1.19953.1956
43.8064-0.2249-1.13097.09550.74152.6045-0.1678-0.08190.3957-0.10850.05090.1734-0.20540.43880.117-0.2647-0.1575-0.0752-0.10080.0312-0.2568-42.0826-0.188242.3406
54.70831.1739-2.2544.0324-1.15439.48850.1247-0.1746-0.1051-0.223-0.51040.3894-1.06680.55820.3858-0.0579-0.1536-0.2214-0.5037-0.0683-0.2794-34.629122.833922.5612
66.67442.5381-2.48644.5479-1.76046.1034-0.254-0.5936-0.7277-0.0544-0.237-0.6343-0.04950.71240.4911-0.32740.0260.00170.2320.148-0.1169-21.5559-4.781240.6113
76.1856-2.4823-1.046.72550.57496.06680.0027-0.01580.7306-0.4888-0.0558-0.0842-0.94130.43470.05310.2046-0.6548-0.1447-0.01730.0359-0.2755-22.354631.462827.9078
810.71383.11010.45855.1576-1.53684.8476-0.5056-0.5563-1.42140.07440.07740.24570.97370.1770.42820.1620.53340.4529-0.18720.1144-0.0368-28.8365-37.518515.636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION2L108 - 211
3X-RAY DIFFRACTION3H1 - 119
4X-RAY DIFFRACTION4A1 - 107
5X-RAY DIFFRACTION5A108 - 211
6X-RAY DIFFRACTION6B1 - 113
7X-RAY DIFFRACTION7B114 - 228
8X-RAY DIFFRACTION8H120 - 228

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