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- PDB-2nr6: Crystal structure of the complex of antibody and the allergen Bla g 2 -

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Basic information

Entry
Database: PDB / ID: 2nr6
TitleCrystal structure of the complex of antibody and the allergen Bla g 2
Components
  • Antibody heavy chain
  • Antibody light chain
  • Aspartic protease Bla g 2
KeywordsHYDROLASE/IMMUNE SYSTEM / Bla g 2 / Fab / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / lysosome / proteolysis / metal ion binding
Similarity search - Function
Immunoglobulin-like - #1960 / Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Immunoglobulins ...Immunoglobulin-like - #1960 / Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Aspartic protease Bla g 2
Similarity search - Component
Biological speciesBlattella germanica (German cockroach)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsLi, M. / Gustchina, A. / Wlodawer, A. / Pomes, A. / Wunschmann, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of a dimerized cockroach allergen Bla g 2 complexed with a monoclonal antibody.
Authors: Li, M. / Gustchina, A. / Alexandratos, J. / Wlodawer, A. / Wunschmann, S. / Kepley, C.L. / Chapman, M.D. / Pomes, A.
History
DepositionNov 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartic protease Bla g 2
B: Aspartic protease Bla g 2
C: Antibody light chain
D: Antibody heavy chain
E: Antibody light chain
F: Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,25212
Polymers164,8306
Non-polymers1,4226
Water1,982110
1
A: Aspartic protease Bla g 2
C: Antibody light chain
D: Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1266
Polymers82,4153
Non-polymers7113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aspartic protease Bla g 2
E: Antibody light chain
F: Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1266
Polymers82,4153
Non-polymers7113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.004, 103.187, 146.329
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUAA-8 - 3271 - 330
21GLYGLYGLUGLUBB-8 - 3271 - 330
12ASPASPARGARGCC1 - 2111 - 211
22ASPASPARGARGEE1 - 2111 - 211
13GLUGLUILEILEDD1 - 2131 - 213
23GLUGLUILEILEFF1 - 2131 - 213

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aspartic protease Bla g 2 / Allergen Bla g II


Mass: 36183.738 Da / Num. of mol.: 2 / Fragment: NIG2 / Mutation: N98Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blattella germanica (German cockroach) / Plasmid: PGAPZAC / Production host: Pichia pastoris (fungus) / Strain (production host): GS115
References: UniProt: P54958, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody Antibody light chain


Mass: 23341.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Pichia pastoris (fungus)
#3: Antibody Antibody heavy chain


Mass: 22889.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Pichia pastoris (fungus)

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 112 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 20% PEG 10000, 0.1M Ammonium sulfate, 5mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 51667 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.098 / Net I/σ(I): 11.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rsym value: 0.301 / % possible all: 65.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1YG9, 1MLB

1yg9

1mlb


Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.841 / SU B: 32.498 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.713 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28058 2610 5.1 %RANDOM
Rwork0.23238 ---
obs0.23478 49052 92.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.47 Å2
2---1.33 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11600 0 86 110 11796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.94816292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44251488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37924.781502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.615151884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6511538
X-RAY DIFFRACTIONr_chiral_restr0.0720.21852
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.24958
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.28002
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2434
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.57636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0212144
X-RAY DIFFRACTIONr_scbond_it034916
X-RAY DIFFRACTIONr_scangle_it04.54148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2536medium positional0.320.5
2C1641medium positional0.290.5
3D1611medium positional0.40.5
1A2536medium thermal02
2C1641medium thermal02
3D1611medium thermal02
LS refinement shellResolution: 2.81→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 102 -
Rwork0.334 2232 -
obs--57.46 %
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)
13.9023-0.4805-0.03271.0316-0.26230.9114-0.0689-0.20030.26020.06440.0395-0.0091-0.02340.0090.0294-0.3547-0.0170.0274-0.3241-0.0079-0.2182-12.17516.886-63.216
24.67920.4377-0.15830.97930.39250.9803-0.09850.00390.04420.02290.079-0.00210.0046-0.01840.0195-0.2940.01680.0232-0.1989-0.0171-0.21936.51923.55-30.128
32.04780.1022-0.37443.1158-0.78861.499-0.05390.4869-0.081-0.845-0.1411-0.67880.00570.41390.1951-0.1275-0.0040.1301-0.0561-0.0271-0.022535.34927.732-92.182
42.2816-1.1761-1.10172.83641.02181.8412-0.1472-0.46540.43260.3662-0.05130.2911-0.307-0.27390.1985-0.1230.0812-0.07970.1832-0.16220.0366-41.02343.97-6.858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-8 - 3271 - 330
2X-RAY DIFFRACTION2BB-8 - 3271 - 330
3X-RAY DIFFRACTION3CC1 - 2111 - 211
4X-RAY DIFFRACTION3DD1 - 2131 - 213
5X-RAY DIFFRACTION4EE1 - 2111 - 211
6X-RAY DIFFRACTION4FF1 - 2131 - 213

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