[English] 日本語
Yorodumi
- PDB-7qwi: Vanadate complex of the vanadium-dependent bromoperoxidase from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qwi
TitleVanadate complex of the vanadium-dependent bromoperoxidase from Corallina pilulifera
ComponentsVanadium-dependent bromoperoxidase
KeywordsOXIDOREDUCTASE / Vanadium protein / halogen binding / haloperoxidase.
Function / homology
Function and homology information


bromide peroxidase / bromide peroxidase activity / metal ion binding
Similarity search - Function
Bromoperoxidase/chloroperoxidase C-terminal / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / BROMIDE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / VANADATE ION / Vanadium-dependent bromoperoxidase
Similarity search - Component
Biological speciesCorallina pilulifera (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsIsupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: R396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera
Authors: Isupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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.beg_label_asym_id ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,20393
Polymers262,4594
Non-polymers6,74489
Water53,1802952
1
AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules

AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules

AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 808 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)807,608279
Polymers787,37612
Non-polymers20,232267
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area140960 Å2
ΔGint-417 kcal/mol
Surface area203250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.601, 199.601, 199.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11DDD-601-

NA

21BBB-1353-

HOH

31BBB-1392-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 2 - 598 / Label seq-ID: 2 - 598

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
221BBBB
332AAAA
442CCCC
553AAAA
663DDDD
774BBBB
884CCCC
995BBBB
10105DDDD
11116CCCC
12126DDDD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

-
Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Vanadium-dependent bromoperoxidase / V-BPO / Vanadium haloperoxidase


Mass: 65614.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corallina pilulifera (eukaryote) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O81959, bromide peroxidase

-
Non-polymers , 9 types, 3041 molecules

#2: Chemical
ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2952 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris-H2SO4, pH 6.8, 0.4M KBr, 1mM Na3VO4, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.92 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.15→14.965 Å / Num. obs: 142571 / % possible obs: 96.4 % / Redundancy: 4.9 % / CC1/2: 0.977 / Rsym value: 0.155 / Net I/σ(I): 8.1
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 2680 / CC1/2: 0.809 / Rsym value: 0.502

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1up8

1up8


Resolution: 2.15→14.965 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.131 / SU B: 4.775 / SU ML: 0.122 / Average fsc free: 0.9389 / Average fsc work: 0.9526 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.173 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1945 7104 5.022 %
Rwork0.1443 134358 -
all0.147 --
obs-141462 98.889 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.248 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→14.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18448 0 365 2952 21765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01219633
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.65226648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08152519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49823.481043
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.457153119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.83615112
X-RAY DIFFRACTIONr_chiral_restr0.0910.22552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215156
X-RAY DIFFRACTIONr_nbd_refined0.2080.210469
X-RAY DIFFRACTIONr_nbtor_refined0.3120.213468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.22388
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.220
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.2180
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.289
X-RAY DIFFRACTIONr_mcbond_it3.2484.4789696
X-RAY DIFFRACTIONr_mcangle_it3.8097.48412152
X-RAY DIFFRACTIONr_scbond_it5.5825.0459936
X-RAY DIFFRACTIONr_scangle_it6.4698.05914432
X-RAY DIFFRACTIONr_lrange_it6.98533.41890367
X-RAY DIFFRACTIONr_ncsr_local_group_10.0540.0520441
X-RAY DIFFRACTIONr_ncsr_local_group_20.0440.0520482
X-RAY DIFFRACTIONr_ncsr_local_group_30.0520.0520448
X-RAY DIFFRACTIONr_ncsr_local_group_40.0530.0520347
X-RAY DIFFRACTIONr_ncsr_local_group_50.050.0520410
X-RAY DIFFRACTIONr_ncsr_local_group_60.0520.0520391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.053560.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.053560.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.043730.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.043730.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.052340.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.052340.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.052510.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.052510.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.050290.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.050290.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.052250.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.052250.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.2495290.1879926X-RAY DIFFRACTION99.6189
2.206-2.2660.2245310.1759679X-RAY DIFFRACTION99.4255
2.266-2.3320.2434900.179405X-RAY DIFFRACTION99.3574
2.332-2.4040.2124950.1559090X-RAY DIFFRACTION99.3676
2.404-2.4830.2314630.1588896X-RAY DIFFRACTION99.2997
2.483-2.570.2244380.1578577X-RAY DIFFRACTION99.2951
2.57-2.6670.2374340.1528272X-RAY DIFFRACTION99.0218
2.667-2.7760.2184390.1537886X-RAY DIFFRACTION98.9422
2.776-2.8990.234100.1517650X-RAY DIFFRACTION98.9321
2.899-3.040.2253510.1587244X-RAY DIFFRACTION98.4701
3.04-3.2050.1913760.1586970X-RAY DIFFRACTION99.1898
3.205-3.3990.2013750.1566619X-RAY DIFFRACTION99.5445
3.399-3.6340.1773260.1346183X-RAY DIFFRACTION99.3134
3.634-3.9240.1662930.1225776X-RAY DIFFRACTION98.9726
3.924-4.2990.1472840.1075294X-RAY DIFFRACTION98.6733
4.299-4.8060.1262340.1014857X-RAY DIFFRACTION99.0082
4.806-5.5480.1422290.1074304X-RAY DIFFRACTION99.4733
5.548-6.7920.1551980.1343668X-RAY DIFFRACTION99.6906
6.792-9.5940.1541440.142875X-RAY DIFFRACTION99.7357
9.594-14.9650.172650.1511187X-RAY DIFFRACTION72.0783

+
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