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- PDB-2bk0: Crystal structure of the major celery allergen Api G 1 -

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Basic information

Entry
Database: PDB / ID: 2bk0
TitleCrystal structure of the major celery allergen Api G 1
ComponentsMAJOR ALLERGEN API G 1
KeywordsALLERGEN / MAJOR CELERY ALLERGEN API G 1 / BET V 1-RELATED PROTEIN / CROSS REACTIVE EPITOPES / PATHOGENESIS-RELATED PROTEIN / PLANT DEFENSE
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major allergen Api g 1, isoallergen 1
Similarity search - Component
Biological speciesAPIUM GRAVEOLENS (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchirmer, T. / Hoffmann-Sommergruber, K. / Breiteneder, H. / Markovic-Housley, Z.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the Major Celery Allergen Api G 1: Molecular Analysis of Cross-Reactivity.
Authors: Schirmer, T. / Hoffmann-Somergrube, K. / Susani, M. / Breiteneder, H. / Markovic-Housley, Z.
History
DepositionFeb 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other / Structure summary
Category: diffrn_source / exptl_crystal_grow ...diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct / struct_biol
Item: _diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.method ..._diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct.title
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR ALLERGEN API G 1
B: MAJOR ALLERGEN API G 1


Theoretical massNumber of molelcules
Total (without water)32,6692
Polymers32,6692
Non-polymers00
Water0
1
A: MAJOR ALLERGEN API G 1


Theoretical massNumber of molelcules
Total (without water)16,3351
Polymers16,3351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MAJOR ALLERGEN API G 1


Theoretical massNumber of molelcules
Total (without water)16,3351
Polymers16,3351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.878, 67.947, 48.001
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA2 - 82 - 8
21GLYGLYLEULEUBB2 - 82 - 8
12LYSLYSGLYGLYAA18 - 2218 - 22
22LYSLYSGLYGLYBB18 - 2218 - 22
13PHEPHEVALVALAA23 - 3023 - 30
23PHEPHEVALVALBB23 - 3023 - 30
14ILEILELEULEUAA44 - 6944 - 69
24ILEILELEULEUBB44 - 6944 - 69
15ILEILEGLYGLYAA71 - 9371 - 93
25ILEILEGLYGLYBB71 - 9371 - 93
16ILEILEHISHISAA95 - 12195 - 121
26ILEILEHISHISBB95 - 12195 - 121
17ASNASNALAALAAA132 - 146132 - 146
27ASNASNALAALABB132 - 146132 - 146

NCS oper: (Code: given
Matrix: (0.2428, -0.79262, -0.55929), (-0.84552, -0.45555, 0.27854), (-0.47555, 0.40526, -0.78078)
Vector: 68.442, 55.422, 76.57)

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Components

#1: Protein MAJOR ALLERGEN API G 1 / CELERY ALLERGEN API G 1 / API G 1.0101 / API G I


Mass: 16334.585 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APIUM GRAVEOLENS (plant) / Tissue: BULB / Plasmid: PMW175 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49372
Compound detailsALLERGEN: PROVOCATES AN ALLERGIC REACTION IN HUMAN
Sequence detailsN-TERMINAL MET MISSING

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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: 2.5 Å3/Da / Density % sol: 35.9 %
Crystal growMethod: vapor diffusion / pH: 6.5
Details: VAPOUR DIFFUSION. RESERVOIR: 10% DIOXANE, 0.1M MES (PH 6.5), 1.6 M AMMONIUM SULFATE. PROTEIN: 35MG/ML IN 28 MM SODIUM PHOSPHATE (PH 7.0).

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ROTATING GENERATOR / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: OSMICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→36.96 Å / Num. obs: 7549 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 1.65 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.83 Å / Redundancy: 1.59 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.36 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BV1

1bv1


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU ML: 0.404 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 315 4.6 %RANDOM
Rwork0.221 ---
obs0.224 6567 90 %-
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: 21.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20.84 Å2
2--4.53 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 0 0 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222230
X-RAY DIFFRACTIONr_bond_other_d0.0010.022051
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9733044
X-RAY DIFFRACTIONr_angle_other_deg0.94134760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.96126.4178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52715340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.267152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_nbd_refined0.1890.2383
X-RAY DIFFRACTIONr_nbd_other0.1790.21848
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21084
X-RAY DIFFRACTIONr_nbtor_other0.0850.21317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2431.51948
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.27422419
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3463813
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5754.5625
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1521 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.060.05
tight thermal0.080.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 20
Rwork0.326 513
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)
13.1741.2498-0.13593.14161.07162.32020.08430.0652-0.41910.075-0.33050.62070.3576-0.27240.24620.2484-0.0515-0.06660.3951-0.10940.454938.274-0.69822.617
27.7761.5089-2.06672.73870.07444.85430.4443-0.64480.92250.23740.0729-0.1814-0.67090.6485-0.51730.3512-0.21710.03330.4822-0.15590.370365.28729.7740.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 154
2X-RAY DIFFRACTION2B2 - 154

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