[English] 日本語
Yorodumi
- PDB-6l8s: High resolution crystal structure of crustacean hemocyanin. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l8s
TitleHigh resolution crystal structure of crustacean hemocyanin.
Components(Hemocyanin) x 3
KeywordsOXYGEN TRANSPORT / Copper protein / Hemocyanin / Phenoloxidase / Crustacean / Arthropod
Function / homology
Function and homology information


Hemocyanin, C-terminal domain / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN ATOM
Similarity search - Component
Biological speciesPanulirus japonicus (Japanese spiny lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMasuda, T. / Mikami, B. / Baba, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science19K06221 Japan
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: The high-resolution crystal structure of lobster hemocyanin shows its enzymatic capability as a phenoloxidase.
Authors: Masuda, T. / Baba, S. / Matsuo, K. / Ito, S. / Mikami, B.
History
DepositionNov 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_ptnr1_label_alt_id / _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 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemocyanin
B: Hemocyanin
C: Hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,24043
Polymers223,8203
Non-polymers2,42040
Water24,0141333
1
A: Hemocyanin
B: Hemocyanin
C: Hemocyanin
hetero molecules

A: Hemocyanin
B: Hemocyanin
C: Hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,48086
Polymers447,6406
Non-polymers4,84080
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)119.454, 207.596, 187.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1043-

HOH

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein Hemocyanin /


Mass: 74643.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB LC505511
Source: (natural) Panulirus japonicus (Japanese spiny lobster)
#2: Protein Hemocyanin /


Mass: 74611.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB LC505511
Source: (natural) Panulirus japonicus (Japanese spiny lobster)
#3: Protein Hemocyanin /


Mass: 74565.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB LC505511
Source: (natural) Panulirus japonicus (Japanese spiny lobster)

-
Sugars , 1 types, 2 molecules

#5: 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.: 2
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 , 7 types, 1371 molecules

#4: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1333 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Lithium sulfate monohydrate, Sodium citrate tribasic dihydrate, PEG1,000, magnesium chloride,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→42.695 Å / Num. obs: 615236 / % possible obs: 99.7 % / Redundancy: 3.78 % / Biso Wilson estimate: 21.86 Å2 / CC1/2: 0.754 / Net I/σ(I): 15.24
Reflection shellResolution: 1.58→1.68 Å / Rmerge(I) obs: 0.464 / Num. unique obs: 99005

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HCY

1hcy


Resolution: 1.58→42.695 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 18.77
RfactorNum. reflection% reflection
Rfree0.1862 30281 4.92 %
Rwork0.1489 --
obs0.1507 615190 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.59 Å2 / Biso mean: 28.8303 Å2 / Biso min: 12.01 Å2
Refinement stepCycle: final / Resolution: 1.58→42.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15788 0 129 1333 17250
Biso mean--44.23 35.78 -
Num. residues----1950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.5980.349210900.28291908697
1.598-1.61680.286610110.232719409100
1.6168-1.63650.26259830.220119588100
1.6365-1.65720.275811170.21219397100
1.6572-1.6790.24138890.196919598100
1.679-1.7020.229910470.179319557100
1.702-1.72630.23538630.177619684100
1.7263-1.75210.224210780.169419425100
1.7521-1.77950.206210370.165419567100
1.7795-1.80860.19949860.159219542100
1.8086-1.83980.207810060.160419560100
1.8398-1.87330.19229300.148119603100
1.8733-1.90930.19679970.145119512100
1.9093-1.94830.20410400.141319488100
1.9483-1.99060.199110020.136319577100
1.9906-2.03690.196210790.140719442100
2.0369-2.08790.18519970.138219476100
2.0879-2.14430.17679080.135619641100
2.1443-2.20740.190910050.131519566100
2.2074-2.27870.183710200.133219439100
2.2787-2.36010.178410350.134819554100
2.3601-2.45460.180710200.144619503100
2.4546-2.56630.17610220.139219502100
2.5663-2.70160.19059610.14719525100
2.7016-2.87080.196510530.154919476100
2.8708-3.09240.205210980.167419402100
3.0924-3.40350.201910710.160519486100
3.4035-3.89570.15529280.137419544100
3.8957-4.9070.14189240.125419568100
4.907-42.6950.169110840.15471919299

+
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