[English] 日本語
Yorodumi
- PDB-1jer: CUCUMBER STELLACYANIN, CU2+, PH 7.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jer
TitleCUCUMBER STELLACYANIN, CU2+, PH 7.0
ComponentsCUCUMBER STELLACYANIN
KeywordsELECTRON TRANSPORT / COPPER / GLYCOPROTEIN / HYDROXYLATION
Function / homology
Function and homology information


electron transfer activity / metal ion binding
Similarity search - Function
Phytocyanin domain / Phytocyanin / Plastocyanin-like domain / Phytocyanin domain profile. / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Cucumber peeling cupredoxin
Similarity search - Component
Biological speciesCucumis sativus (cucumber)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsHart, P.J. / Nersissian, A.M. / Herrmann, R.G. / Nalbandyan, R.M. / Valentine, J.S. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 1996
Title: A missing link in cupredoxins: crystal structure of cucumber stellacyanin at 1.6 A resolution.
Authors: Hart, P.J. / Nersissian, A.M. / Herrmann, R.G. / Nalbandyan, R.M. / Valentine, J.S. / Eisenberg, D.
#1: Journal: To be Published
Title: Cloning, Expression, and Spectroscopic Characterization of Cucumis Sativus Stellacyanin in its Non-Glycosylated Form
Authors: Nersissian, A.M. / Mehrabian, Z.B. / Nalbandyan, R.M. / Hart, P.J. / Fraczkiewicz, G. / Czernuszewicz, R.S. / Bender, C.J. / Peisach, J. / Herrmann, R.G. / Valentine, J.S.
History
DepositionAug 21, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CUCUMBER STELLACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9532
Polymers14,8901
Non-polymers641
Water1,964109
1
A: CUCUMBER STELLACYANIN
hetero molecules

A: CUCUMBER STELLACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9064
Polymers29,7792
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+4/31
Unit cell
Length a, b, c (Å)59.180, 59.180, 74.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-139-

HOH

-
Components

#1: Protein CUCUMBER STELLACYANIN / CUCUMBER PEELING CUPREDOXIN


Mass: 14889.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FROM CUCUMBER PEELINGS, GLUTAMINE AXIAL COPPER LIGAND
Source: (gene. exp.) Cucumis sativus (cucumber) / Cell line: BL21 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P29602
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 60.7 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
129 mg/mlprotein1drop
27.1 mMacetate1drop
329 mMHEPES1drop
40.69 Mammonium sulfate1drop
5100 mMHEPES1reservoir
62.4 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 3, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 18488 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.3
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 1.4 / % possible all: 53.5
Reflection
*PLUS
Num. measured all: 82930
Reflection shell
*PLUS
% possible obs: 53.5 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementResolution: 1.6→50 Å / σ(F): 0
Details: RESIDUES 65 - 70 HAVE HIGH THERMAL PARAMETERS, AND ARE THUS MODELED POORLY. THE POSITION OF THE MAIN CHAIN IS ROUGHLY CORRECT, BUT SIDE CHAIN DENSITY IS DIFFICULT TO INTERPRET. ALL OUTLIERS ...Details: RESIDUES 65 - 70 HAVE HIGH THERMAL PARAMETERS, AND ARE THUS MODELED POORLY. THE POSITION OF THE MAIN CHAIN IS ROUGHLY CORRECT, BUT SIDE CHAIN DENSITY IS DIFFICULT TO INTERPRET. ALL OUTLIERS IN THE RAMACHANDRAN PLOT(3) COME FROM THIS REGION OF THE PROTEIN.
RfactorNum. reflection% reflection
Rfree0.237 --
all0.195 18488 -
obs0.193 -90.9 %
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 1 109 962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d2.5
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

+
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