[English] 日本語
Yorodumi
- PDB-3qjo: Refined Structure of the functional unit (KLH1-H) of keyhole limp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qjo
TitleRefined Structure of the functional unit (KLH1-H) of keyhole limpet hemocyanin
ComponentsHemocyanin 1
KeywordsOXYGEN BINDING / PF00264 / hemolymph
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2570 / Haemocyanin C-terminal domain / Hemocyanin; Chain: A, domain 2 / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase ...Immunoglobulin-like - #2570 / Haemocyanin C-terminal domain / Hemocyanin; Chain: A, domain 2 / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Hemocyanin 1 / Hemocyanin 1
Similarity search - Component
Biological speciesMegathura crenulata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsJaenicke, E. / Buchler, K. / Decker, H. / Markl, J. / Schroder, G.F.
Citation
Journal: Iubmb Life / Year: 2011
Title: The refined structure of functional unit h of keyhole limpet hemocyanin (KLH1-h) reveals disulfide bridges.
Authors: Jaenicke, E. / Buchler, K. / Decker, H. / Markl, J. / Schroder, G.F.
#1: Journal: Biochem.J. / Year: 2010
Title: Cupredoxin-like domains in haemocyanins.
Authors: Jaenicke, E. / Buchler, K. / Markl, J. / Decker, H. / Barends, T.R.
History
DepositionJan 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_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_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Hemocyanin 1
B: Hemocyanin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5026
Polymers113,2482
Non-polymers2544
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-17 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)251.020, 251.020, 251.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein Hemocyanin 1


Mass: 56623.797 Da / Num. of mol.: 2 / Fragment: collar subunit (UNP RESIDUES 2912-3406) / Source method: isolated from a natural source / Source: (natural) Megathura crenulata (invertebrata) / References: UniProt: Q53IP9, UniProt: Q10583*PLUS
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.82 Å3/Da / Density % sol: 78.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 9% PEG 1000, 50mM phosphate/citrate buffer, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 22294 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.18
Reflection shellResolution: 4→4.2 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 3.46 / % possible all: 96.4

-
Processing

Software
NameClassification
MAR345data collection
PHASERphasing
RESOLVEmodel building
DMmodel building
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RESOLVEphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JS8, 2CBP

1js8

2cbp


Resolution: 4→30 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: DEN refinement
RfactorNum. reflectionSelection details
Rfree0.2933 1872 RANDOM
Rwork0.2712 --
all0.2731 22363 -
obs0.2731 22294 -
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7990 0 4 0 7994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.855
X-RAY DIFFRACTIONc_bond_d0.003382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
4-4.140.43841740.3965X-RAY DIFFRACTION22053
4.14-4.310.3961530.3855X-RAY DIFFRACTION22343
4.31-4.50.34181810.3393X-RAY DIFFRACTION22003

+
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://pdbjlvh1.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