[English] 日本語
Yorodumi
- PDB-4pve: Wild-type Phl p 4.0202, a glucose dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pve
TitleWild-type Phl p 4.0202, a glucose dehydrogenase
ComponentsPollen allergen Phl p 4.0202
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / BI-COVALENT FLAVINYLATION / ALLERGEN / GLUCOSE DEHYDROGENASE / LOW OXYGEN REACTIVITY / GRASS POLLEN
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / MALONATE ION / Pollen allergen Phl p 4.0202
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZafred, D. / Teufelberger, A. / Keller, W. / Macheroux, P.
CitationJournal: Febs J. / Year: 2015
Title: Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction.
Authors: Zafred, D. / Steiner, B. / Teufelberger, A.R. / Hromic, A. / Karplus, P.A. / Schofield, C.J. / Wallner, S. / Macheroux, P.
History
DepositionMar 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Apr 22, 2015Group: Structure summary
Revision 1.4Jun 3, 2015Group: Other
Revision 1.5Sep 2, 2015Group: Database references
Revision 1.6Nov 22, 2017Group: Refinement description / Category: software
Revision 1.7Sep 20, 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_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pollen allergen Phl p 4.0202
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8027
Polymers55,7311
Non-polymers1,0716
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.220, 117.220, 201.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21A-1162-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Pollen allergen Phl p 4.0202


Mass: 55730.703 Da / Num. of mol.: 1 / Fragment: Phl p 4.0202 / Mutation: N61Q, N330Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: phlp4 / Production host: Komagataella pastoris (fungus) / References: UniProt: B2ZWE9

-
Non-polymers , 5 types, 626 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7 mg/mL Protein in 20mM Tris + 70% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 159723 / Num. obs: 159693 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.4→1.5 Å / Mean I/σ(I) obs: 0.84 / Num. unique all: 29439 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERmrphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3TSH

3tsh


Resolution: 1.5→49.22 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 13.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1542 6512 5 %random
Rwork0.1317 ---
obs0.1328 130251 99.98 %-
all-159723 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 70 620 4542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094111
X-RAY DIFFRACTIONf_angle_d1.3175594
X-RAY DIFFRACTIONf_dihedral_angle_d14.321509
X-RAY DIFFRACTIONf_chiral_restr0.052596
X-RAY DIFFRACTIONf_plane_restr0.008714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.2462140.21634061X-RAY DIFFRACTION100
1.517-1.53490.25092130.20054045X-RAY DIFFRACTION100
1.5349-1.55360.22432150.19134075X-RAY DIFFRACTION100
1.5536-1.57330.1952130.18664061X-RAY DIFFRACTION100
1.5733-1.5940.21082140.18394060X-RAY DIFFRACTION100
1.594-1.61580.19922140.17354067X-RAY DIFFRACTION100
1.6158-1.63890.18732150.17084077X-RAY DIFFRACTION100
1.6389-1.66340.22192140.16594065X-RAY DIFFRACTION100
1.6634-1.68940.18492150.14114097X-RAY DIFFRACTION100
1.6894-1.71710.16852140.13394061X-RAY DIFFRACTION100
1.7171-1.74670.14762150.1294075X-RAY DIFFRACTION100
1.7467-1.77840.15982160.12654113X-RAY DIFFRACTION100
1.7784-1.81260.15872140.11984064X-RAY DIFFRACTION100
1.8126-1.84960.15472160.11864097X-RAY DIFFRACTION100
1.8496-1.88990.16332140.12064079X-RAY DIFFRACTION100
1.8899-1.93380.14672160.12244092X-RAY DIFFRACTION100
1.9338-1.98220.15442160.1244101X-RAY DIFFRACTION100
1.9822-2.03580.16662150.12254103X-RAY DIFFRACTION100
2.0358-2.09570.12672170.11514117X-RAY DIFFRACTION100
2.0957-2.16330.15492160.11674107X-RAY DIFFRACTION100
2.1633-2.24070.13532180.11084129X-RAY DIFFRACTION100
2.2407-2.33040.1522170.11344120X-RAY DIFFRACTION100
2.3304-2.43640.13752170.11544140X-RAY DIFFRACTION100
2.4364-2.56490.14932190.12384145X-RAY DIFFRACTION100
2.5649-2.72560.14282190.12644166X-RAY DIFFRACTION100
2.7256-2.9360.17322200.13514183X-RAY DIFFRACTION100
2.936-3.23140.1422200.14464189X-RAY DIFFRACTION100
3.2314-3.69880.14112230.13574230X-RAY DIFFRACTION100
3.6988-4.65960.14372260.11484292X-RAY DIFFRACTION100
4.6596-49.24650.15082370.14494528X-RAY DIFFRACTION100

+
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