[English] 日本語
Yorodumi
- PDB-3wky: Crystal structure of hemolymph type prophenoloxidase (proPOb) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wky
TitleCrystal structure of hemolymph type prophenoloxidase (proPOb) from crustacean
ComponentsProphenoloxidase b
KeywordsOXIDOREDUCTASE ACTIVATOR / type 3 copper protein / phenoloxidase / tyrosinase / hydroxydation / monophenols / oxidation / o-diphenols / plasma
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Hemocyanin, N-terminal domain / Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal ...Hemocyanin, N-terminal domain / Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Hemocyanin, N-terminal domain / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin E-set / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CU2-O2 CLUSTER / Prophenoloxidase b
Similarity search - Component
Biological speciesMarsupenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsMasuda, T. / Mikami, B.
CitationJournal: Febs J. / Year: 2014
Title: The crystal structure of a crustacean prophenoloxidase provides a clue to understanding the functionality of the type 3 copper proteins.
Authors: Masuda, T. / Momoji, K. / Hirata, T. / Mikami, B.
History
DepositionNov 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prophenoloxidase b
B: Prophenoloxidase b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,95932
Polymers157,7972
Non-polymers4,16230
Water21,2041177
1
A: Prophenoloxidase b
B: Prophenoloxidase b
hetero molecules

A: Prophenoloxidase b
B: Prophenoloxidase b
hetero molecules

A: Prophenoloxidase b
B: Prophenoloxidase b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,87896
Polymers473,3916
Non-polymers12,48790
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area48780 Å2
ΔGint-136 kcal/mol
Surface area145870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.706, 156.706, 283.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Prophenoloxidase b


Mass: 78898.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marsupenaeus japonicus (crustacean) / Secretion: hemolymph plasma / References: UniProt: G5EKM4

-
Sugars , 2 types, 12 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 1195 molecules

#4: Chemical ChemComp-CUO / CU2-O2 CLUSTER / CU-O2-CU LINKAGE


Mass: 159.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1177 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE AUTHOR STATES THAT THE STRUCTURAL FACTOR AND REFINED STRUCTURE CLEARLY SUGGESTED THAT THIS ...THE AUTHOR STATES THAT THE STRUCTURAL FACTOR AND REFINED STRUCTURE CLEARLY SUGGESTED THAT THIS POSITION IS DEFINITELY ARG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1M Sodium malonate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2001 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 240286 / Num. obs: 239565 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.8630.4772.46198.4
1.86-1.943.30.3793.68199.7
1.94-2.033.40.2745.34199.8
2.03-2.133.40.1857.92199.9
2.13-2.273.40.13211.3199.9
2.27-2.443.40.09815.31100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.801→34.806 Å / SU ML: 0.17 / σ(F): 1.96 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 11998 5.01 %
Rwork0.1747 --
obs0.1757 239452 99.59 %
all-239565 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→34.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10649 0 247 1177 12073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712003
X-RAY DIFFRACTIONf_angle_d1.10816498
X-RAY DIFFRACTIONf_dihedral_angle_d15.2584666
X-RAY DIFFRACTIONf_chiral_restr0.0771799
X-RAY DIFFRACTIONf_plane_restr0.0052142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8009-1.82140.27413530.26127204X-RAY DIFFRACTION94
1.8214-1.84280.28973660.25077554X-RAY DIFFRACTION99
1.8428-1.86530.25984120.24447490X-RAY DIFFRACTION99
1.8653-1.88890.26693900.23067592X-RAY DIFFRACTION100
1.8889-1.91370.24843820.22187588X-RAY DIFFRACTION100
1.9137-1.93990.25764110.22257602X-RAY DIFFRACTION100
1.9399-1.96760.23734340.21957520X-RAY DIFFRACTION100
1.9676-1.9970.21113880.2057594X-RAY DIFFRACTION100
1.997-2.02820.2583880.20257613X-RAY DIFFRACTION100
2.0282-2.06150.23334020.19657658X-RAY DIFFRACTION100
2.0615-2.0970.21184140.19287498X-RAY DIFFRACTION100
2.097-2.13510.21963770.18887661X-RAY DIFFRACTION100
2.1351-2.17620.2053870.18467671X-RAY DIFFRACTION100
2.1762-2.22060.2084190.187606X-RAY DIFFRACTION100
2.2206-2.26890.20514040.18287551X-RAY DIFFRACTION100
2.2689-2.32160.2024050.1787601X-RAY DIFFRACTION100
2.3216-2.37970.20434130.17997648X-RAY DIFFRACTION100
2.3797-2.4440.19814360.17957552X-RAY DIFFRACTION100
2.444-2.51590.19174500.16897576X-RAY DIFFRACTION100
2.5159-2.59710.20953980.17277574X-RAY DIFFRACTION100
2.5971-2.68990.18974340.17887619X-RAY DIFFRACTION100
2.6899-2.79750.18474090.17077656X-RAY DIFFRACTION100
2.7975-2.92480.19573880.17877571X-RAY DIFFRACTION100
2.9248-3.07890.19753910.17957593X-RAY DIFFRACTION100
3.0789-3.27170.20133840.17877683X-RAY DIFFRACTION100
3.2717-3.52410.17954080.1597589X-RAY DIFFRACTION100
3.5241-3.87830.1633580.14367614X-RAY DIFFRACTION100
3.8783-4.43850.14983860.13677638X-RAY DIFFRACTION100
4.4385-5.58830.15293850.13777640X-RAY DIFFRACTION100
5.5883-34.81290.19394260.18267498X-RAY DIFFRACTION99

+
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