[English] 日本語
Yorodumi
- PDB-1j2v: Crystal Structure of CutA1 from Pyrococcus Horikoshii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j2v
TitleCrystal Structure of CutA1 from Pyrococcus Horikoshii
Components102AA long hypothetical periplasmic divalent cation tolerance protein CUTA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA + BETA
Function / homology
Function and homology information


response to metal ion / copper ion binding / cytoplasm
Similarity search - Function
: / Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsTanaka, Y. / Sakai, N. / Yasutake, Y. / Yao, M. / Tsumoto, K. / Kumagai, I. / Tanaka, I.
CitationJournal: Febs Lett. / Year: 2004
Title: Structural implications for heavy metal-induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA.
Authors: Tanaka, Y. / Tsumoto, K. / Nakanishi, T. / Yasutake, Y. / Sakai, N. / Yao, M. / Tanaka, I. / Kumagai, I.
History
DepositionJan 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA


Theoretical massNumber of molelcules
Total (without water)12,4791
Polymers12,4791
Non-polymers00
Water64936
1
A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA

A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA

A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA


Theoretical massNumber of molelcules
Total (without water)37,4373
Polymers37,4373
Non-polymers00
Water543
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 area6380 Å2
ΔGint-44 kcal/mol
Surface area13070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.569, 52.569, 58.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: (1-y, 1+x-y, z) and (y-x, 1-x, z).

-
Components

#1: Protein 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA / CutA1 / CutA1 homology protein PH0992


Mass: 12479.017 Da / Num. of mol.: 1 / Mutation: L26(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0992 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O58720
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium Sulfate , Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9000, 0.9792, 0.9794
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2002
RadiationMonochromator: MONOCHROMATOR + MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97921
30.97941
ReflectionResolution: 2→20 Å / Num. all: 6186 / Num. obs: 6154 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 11.2 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.058 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 901 / Rsym value: 0.112 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
DMmodel building
CNS1refinement
HKL-2000data reduction
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Model refinement was performed with a twinning operator of (h -h-k -l), and a twinning fraction of 0.16.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 589 9.5 %RANDOM
Rwork0.239 ---
all-6122 --
obs-6114 98.9 %-
Displacement parametersBiso mean: 23.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.846 Å2-1.067 Å20 Å2
2---0.846 Å20 Å2
3---1.692 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 0 36 909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013115
X-RAY DIFFRACTIONc_angle_deg1.90039
X-RAY DIFFRACTIONc_dihedral_angle_d23.7386
X-RAY DIFFRACTIONc_improper_angle_d1.76773
X-RAY DIFFRACTIONc_mcbond_it1.26
X-RAY DIFFRACTIONc_mcangle_it1.73
X-RAY DIFFRACTIONc_scbond_it2.05
X-RAY DIFFRACTIONc_scangle_it2.63
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.379 64 -
Rwork0.292 607 -
obs-607 99 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

+
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