[English] 日本語
Yorodumi
- PDB-2vxq: Crystal structure of the major grass pollen allergen Phl p 2 in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vxq
TitleCrystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab
Components
  • (FABFragment antigen-binding) x 2
  • POLLEN ALLERGEN PHL P 2
KeywordsALLERGEN / RECEPTOR / SECRETED / RPHL P 2 / ALLERGEN-IGE FAB COMPLEX / RECOMBINANT GRASS POLLEN ALLERGEN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Pollen allergen Lol p2 / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin, cellulose-binding-like domain / Expansin, cellulose-binding-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pollen allergen Phl p 2
Similarity search - Component
Biological speciesPHLEUM PRATENSE (timothy grass)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPadavattan, S. / Flicker, S. / Schirmer, T. / Madritsch, C. / Randow, S. / Reese, G. / Vieths, S. / Lupinek, C. / Ebner, C. / Valenta, R. / Markovic-Housley, Z.
CitationJournal: J.Immunol. / Year: 2009
Title: High-Affinity Ige Recognition of a Conformational Epitope of the Major Respiratory Allergen Phl P 2 as Revealed by X-Ray Crystallography.
Authors: Padavattan, S. / Flicker, S. / Schirmer, T. / Madritsch, C. / Randow, S. / Reese, G. / Vieths, S. / Lupinek, C. / Ebner, C. / Valenta, R. / Markovic-Housley, Z.
History
DepositionJul 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.REMARK 999

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLLEN ALLERGEN PHL P 2
H: FAB
L: FAB


Theoretical massNumber of molelcules
Total (without water)57,2503
Polymers57,2503
Non-polymers00
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-36.4 kcal/mol
Surface area27550 Å2
MethodPQS
Unit cell
Length a, b, c (Å)105.437, 105.437, 110.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11L-2051-

HOH

21L-2065-

HOH

31L-2133-

HOH

-
Components

#1: Protein POLLEN ALLERGEN PHL P 2 / TIMOTHY GRASS POLLEN ALLERGEN PHL P 2 / PHL P II


Mass: 10828.056 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHLEUM PRATENSE (timothy grass) / Plasmid: PMW 172 / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P43214
#2: Antibody FAB / Fragment antigen-binding


Mass: 22976.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: H CHAIN OF THE FAB FRAGMENT COMPOSED OF THE IGE VARIABLE DOMAIN AND IGG CONSTANT DOMAIN
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-LYMPHOCITE / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY
#3: Antibody FAB / Fragment antigen-binding


Mass: 23444.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: L CHAIN OF THE FAB FRAGMENT COMPOSED OF THE IGE VARIABLE DOMAIN AND IGG CONSTANT DOMAIN
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-LYMPHOCITE / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ACCESSION NUMBER AJ458379 REFERS TO THE SEQUENCE OF THE VARIABLE DOMAIN OF THE LIGHT CHAIN ...THE ACCESSION NUMBER AJ458379 REFERS TO THE SEQUENCE OF THE VARIABLE DOMAIN OF THE LIGHT CHAIN (KAPPA).THE ABOVE GIVEN SEQUENCE INCLUDES ALSO THE CONSTANT DOMAIN OF THE LIGHT CHAIN. THE ACCESSION NUMBER AJ458382 REFERS TO THE SEQUENCE OF THE VARIABLE DOMAIN OF THE HEAVY CHAIN. THE ABOVE GIVEN SEQUENCE INCLUDES ALSO THE CONSTANT DOMAIN OF THE HEAVY CHAIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: HANGING DROP DIFFUSION, 1 MICROL PROTEIN (IN 30 MM HEPES, 0.15 M NACL PH 6.8) MIXED WITH 1 MICROL RESERVOIR (20% PEG 3350, 0.2 M NAF)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.9→27.56 Å / Num. obs: 48722 / % possible obs: 98.4 % / Redundancy: 5.53 % / Rmerge(I) obs: 0.077 / Rsym value: 0.07 / Net I/σ(I): 17.89
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.43 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019 24/04/2001refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1U6A, 1WH0

1u6a

1wh0


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.757 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2466 5.06 %RANDOM
Rwork0.177 ---
obs0.179 48678 98.3 %-
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: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2---0.08 Å20 Å2
3---0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 0 524 4491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223960
X-RAY DIFFRACTIONr_bond_other_d0.0030.022611
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9495405
X-RAY DIFFRACTIONr_angle_other_deg0.7833.0036328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0885512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47324.342152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88915582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1158
X-RAY DIFFRACTIONr_chiral_restr0.070.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_nbd_refined0.1930.2712
X-RAY DIFFRACTIONr_nbd_other0.20.22698
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21893
X-RAY DIFFRACTIONr_nbtor_other0.0850.22156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7631.53245
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.36224123
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.18931682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.444.51282
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
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 144
Rwork0.211 2691
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)
11.4576-0.2515-0.13360.93830.32291.1158-0.0883-0.03260.0464-0.05390.0627-0.0248-0.0368-0.01920.0256-0.073-0.0236-0.0192-0.0572-0.0064-0.218215.092-0.985.798
22.9451-1.7595-0.19261.89930.08010.7924-0.322-0.79950.22210.13510.351-0.1470.0110.2146-0.029-0.0440.0373-0.03390.2269-0.091-0.175531.5412.31221.482
36.8738-1.8052-0.10551.24070.3561.4939-0.32810.1199-1.33910.0570.07510.11980.3853-0.07480.25310.0574-0.07990.2036-0.082-0.08750.159140.938-25.036-6.3
43.0754-0.0038-0.08781.34970.19233.4746-0.1403-0.0397-0.2785-0.1227-0.013-0.12020.03190.02290.1532-0.0109-0.02920.0529-0.0644-0.0133-0.13148.098-10.991-1.673
51.7252-1.7278-1.66363.22683.71895.3726-0.0304-0.24020.2829-0.16220.13650.0538-0.47870.1841-0.10610.03180.0085-0.07320.0416-0.1074-0.095310.43620.12126.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2H1 - 121
3X-RAY DIFFRACTION3L109 - 213
4X-RAY DIFFRACTION4H122 - 213
5X-RAY DIFFRACTION5A1 - 94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more