[English] 日本語
Yorodumi
- PDB-5aa6: Homohexameric Structure of the second Vanadate-Dependent Bromoper... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aa6
TitleHomohexameric Structure of the second Vanadate-Dependent Bromoperoxidase (AnII) from Ascophyllum nodosum
ComponentsVANADIUM-DEPENDENT BROMOPEROXIDASE 2
KeywordsOXIDOREDUCTASE / BROWN ALGAE / BROMOPEROXIDASE / VANADIUM-DEPENDANT HALOGENPEROXIDASE
Function / homology
Function and homology information


peroxidase activity
Similarity search - Function
Vanadium-containing Chloroperoxidase, domain 2 / Vanadium-containing Chloroperoxidase; domain 2 / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
VANADATE ION / Vanadium-dependent bromoperoxidase 2
Similarity search - Component
Biological speciesASCOPHYLLUM NODOSUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRadlow, M. / Jeudy, A. / Dabin, J. / Delage, L. / Leblanc, C. / Hartung, J. / Czjzek, M.
Citation
Journal: To be Published
Title: Homohexameric Structure of the Second Vanadate Dependant Bromoperoxidase from Ascophyllum Nodosum
Authors: Radlow, M. / Czjzek, M. / Jeudy, A. / Dabin, J. / Delage, L. / Leblanc, C. / Hartung, J.
#1: Journal: Bioorg.Chem. / Year: 2012
Title: Molecular Cloning, Structure, and Reactivity of the Second Bromoperoxidase from Ascophyllum Nodosum.
Authors: Wischang, D. / Radlow, M. / Schulz, H. / Vilter, H. / Viehweger, L. / Altmeyer, M.O. / Kegler, C. / Herrmann, J. / Muller, R. / Gaillard, F. / Delage, L. / Leblanc, C. / Hartung, J.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
B: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
C: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
D: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
E: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
F: VANADIUM-DEPENDENT BROMOPEROXIDASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,14812
Polymers391,4586
Non-polymers6906
Water36,1562007
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49200 Å2
ΔGint-216.1 kcal/mol
Surface area110310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.790, 236.840, 118.000
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.52, 0.036, -0.853), (-0.786, -0.372, -0.495), (-0.335, 0.928, -0.165)15.049, 18.062, 14.898
2given(-0.529, 0.801, 0.279), (0.787, 0.341, 0.515), (0.318, 0.492, -0.811)-45.006, 8.054, 50.106
3given(0.513, -0.804, -0.3), (0.018, -0.34, 0.94), (-0.858, -0.487, -0.16)10.484, -9.112, 23.538
4given(-0.502, -0.02, 0.865), (0.004, -1, -0.02), (0.865, -0.007, 0.502)-50.045, 26.141, 28.732
5given(-1, -0.026, 0.018), (-0.026, 0.355, -0.934), (0.018, -0.934, -0.356)-34.952, 34.952, 50.515
6given(-0.999527, -0.025133, 0.017739), (-0.02553, 0.355967, -0.93415), (0.017164, -0.93416, -0.356441)-34.98585, 34.11007, 50.53286

-
Components

#1: Protein
VANADIUM-DEPENDENT BROMOPEROXIDASE 2


Mass: 65243.051 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: VANADATE COFACTOR LINKED TO HISTIDINE 536 IN ALL CHAINS. THE BIOLOGICAL MACROMOLECULE HAS THE HOMOHEXAMERIC FORM PRESENT IN THE CRYSTAL STRUCTURE
Source: (natural) ASCOPHYLLUM NODOSUM (eukaryote) / Tissue: CELL WALL (EXTRACELLULAR MATRIX) / References: UniProt: K7ZUA3, bromide peroxidase
#2: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2007 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsVANADATE (VO4): THE VANADATE IS COORDINATED BY HIS 536
Sequence detailsTHE CRYSTAL STRUCTURE CONTAINS A NATIVE PURIFIED PROTEIN FROM THE ORGANISM. THIS FAMILY OF ENZYMES ...THE CRYSTAL STRUCTURE CONTAINS A NATIVE PURIFIED PROTEIN FROM THE ORGANISM. THIS FAMILY OF ENZYMES IS KNOWN TO DISPLAY MANY ISO-FORMS. THE DEDUCED SEQUENCE FROM THE CRYSTAL STRUCTURE DISPLAYS FEW BUT REAL DISCREPANCIES TO THE DEPOSITED SEQUENCE AT UNIPROT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP AT 18 DEGREES C, 2 MICROL OF PROTEIN WITH 1 MICROL RESERVOIR SOLUTION, NACL 0.1 M, BIS-TRIS 0.01 M, PH 5.5 AND 25 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.26→65 Å / Num. obs: 170315 / % possible obs: 98.7 % / Observed criterion σ(I): 0.1 / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QI9

1qi9


Resolution: 2.26→70 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.107 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WERE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23592 8509 5 %RANDOM
Rwork0.16987 ---
obs0.17317 161755 98.62 %-
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: 19.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-1.53 Å2
2---1.25 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.26→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27293 0 30 2007 29330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01928461
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9638803
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04453714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24124.6031349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.712154549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.70215175
X-RAY DIFFRACTIONr_chiral_restr0.1040.24250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122251
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 590 -
Rwork0.258 11815 -
obs--98.48 %

+
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