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Entry
Database: PDB / ID: 3qg6
TitleStructural Basis for Ligand Recognition and Discrimination of a Quorum Quenching Antibody
Components
  • AP4-24H11 Heavy Chain
  • AP4-24H11 Light Chain
  • Agr autoinducing peptide
KeywordsIMMUNE SYSTEM/INHIBITOR / Immunoglobulin Fold / Antigen binding / AIP4 binding / Secreted / IMMUNE SYSTEM-INHIBITOR complex
Function / homologyStaphylococcal AgrD / Staphylococcal AgrD protein / Staphylococcal AgrD protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Agr autoinducing peptide
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKirchdoerfer, R.N. / Janda, J.D. / Kaufmann, G.F. / 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP4-24H11 Light Chain
B: AP4-24H11 Heavy Chain
H: AP4-24H11 Heavy Chain
L: AP4-24H11 Light Chain
C: Agr autoinducing peptide
D: Agr autoinducing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,06017
Polymers96,4256
Non-polymers63511
Water5,296294
1
A: AP4-24H11 Light Chain
B: AP4-24H11 Heavy Chain
D: Agr autoinducing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4978
Polymers48,2133
Non-polymers2855
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-37 kcal/mol
Surface area20030 Å2
MethodPISA
2
H: AP4-24H11 Heavy Chain
L: AP4-24H11 Light Chain
C: Agr autoinducing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5639
Polymers48,2133
Non-polymers3506
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 98.498, 73.670
Angle α, β, γ (deg.)90.00, 114.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21L
12B
22H

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYSAA5 - 2075 - 212
21THRTHRLYSLYSLD5 - 2075 - 212
12GLNGLNTHRTHRBB5 - 1105 - 110
22GLNGLNTHRTHRHC5 - 1105 - 110

NCS ensembles :
ID
1
2

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Components

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Agr autoinducing peptide


Mass: 1027.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the peptide was chemically synthesized / References: UniProt: Q9F6Z3

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Antibody , 2 types, 4 molecules ALBH

#1: Antibody AP4-24H11 Light Chain


Mass: 24137.809 Da / Num. of mol.: 2
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 Heavy Chain


Mass: 23047.609 Da / Num. of mol.: 2
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)

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Non-polymers , 3 types, 305 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 29mM Zinc chloride, 20% PEG 4000, 0.1M sodium cacodylate. Cryoprotection in 20% Glycerol, pH 6.5, 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: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→39.74 Å / Num. all: 29017 / Num. obs: 29017 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.6 / % possible all: 90.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 15C8

15c8


Resolution: 2.5→39.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU B: 18.676 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23877 1477 5.1 %RANDOM
Rwork0.18354 ---
all0.18637 29017 --
obs0.18637 27360 93.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.847 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20.11 Å2
2--0.48 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 11 294 7000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226872
X-RAY DIFFRACTIONr_bond_other_d0.0020.024556
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9669370
X-RAY DIFFRACTIONr_angle_other_deg1.469311162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2335847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53624.135266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.917151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9541526
X-RAY DIFFRACTIONr_chiral_restr0.0860.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217562
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021368
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_it1.3681.54253
X-RAY DIFFRACTIONr_mcbond_other0.1451.51714
X-RAY DIFFRACTIONr_mcangle_it2.71626940
X-RAY DIFFRACTIONr_scbond_it3.96532619
X-RAY DIFFRACTIONr_scangle_it6.8064.52430
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
11A1222medium positional0.090.5
22H622medium positional0.060.5
11A1518loose positional0.535
22H804loose positional0.525
11A1222medium thermal1.382
22H622medium thermal2.282
11A1518loose thermal1.310
22H804loose thermal1.9510
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 92 -
Rwork0.264 1794 -
obs-1794 83.56 %
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)
10.0278-0.05750.03540.35460.30461.03270.00670.00360.0210.02170.01270.0006-0.0006-0.0212-0.01950.06860.00480.02910.01890.01450.070910.748614.29432.4472
20.5274-0.3713-0.02970.56450.21510.13880.0005-0.024-0.02070.02550.0349-0.05140.011-0.0252-0.03540.03390.0067-0.00960.1025-0.01080.0436-3.3083-7.88537.324
30.09830.2145-0.0461.29060.57860.6015-0.0581-0.02480.01930.07070.06850.06440.15120.1352-0.01030.09460.04370.00790.0536-0.01560.031824.0056-3.926634.6123
40.5114-0.02580.29680.0509-0.20530.9669-0.04790.1146-0.05770.01850.0338-0.0112-0.0163-0.04560.01410.10740.024-0.00360.0642-0.00960.030711.4722-9.86331.3782
50.01930.0368-0.06620.14230.11931.0699-0.00960.0037-0.0291-0.0322-0.0252-0.0749-0.0426-0.14890.03480.02030.05080.01370.1692-0.00670.049817.12492.0797-31.7602
60.4168-0.2660.520.5392-0.40830.70310.0397-0.0159-0.0429-0.02210.0233-0.0156-0.021-0.0206-0.0630.10810.00150.03440.01620.00080.052837.557612.2483-4.1447
70.8252-0.17520.55930.1030.12291.2737-0.01240.05230.05280.0674-0.0035-0.01840.23430.03570.01580.0941-0.02610.02240.0549-0.01620.038525.141-17.9631-24.0379
80.2487-0.1829-0.39030.49480.19720.69990.06160.0379-0.0013-0.0126-0.027-0.0204-0.0445-0.0775-0.03450.073-0.0106-0.00050.01880.00350.103929.81441.61725.7419
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 - 212
5X-RAY DIFFRACTION5B1 - 114
6X-RAY DIFFRACTION6B115 - 222
7X-RAY DIFFRACTION7A1 - 108
8X-RAY DIFFRACTION8A109 - 212

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