[English] 日本語
Yorodumi
- PDB-1kr4: Structure Genomics, Protein TM1056, cutA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kr4
TitleStructure Genomics, Protein TM1056, cutA
ComponentsProtein TM1056, cutA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / cutA / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsSavchenko, A. / Zhang, R. / Joachimiak, A. / Edwards, A. / Akarina, T. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2004
Title: X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.
Authors: Savchenko, A. / Skarina, T. / Evdokimova, E. / Watson, J.D. / Laskowski, R. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A. / Zhang, R.G.
History
DepositionJan 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Remark 999SEQUENCE The assignement of Ile94 was based on high resolution electron density maps

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein TM1056, cutA


Theoretical massNumber of molelcules
Total (without water)15,0221
Polymers15,0221
Non-polymers00
Water2,252125
1
A: Protein TM1056, cutA

A: Protein TM1056, cutA

A: Protein TM1056, cutA


Theoretical massNumber of molelcules
Total (without water)45,0653
Polymers45,0653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.237, 52.237, 33.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein Protein TM1056, cutA


Mass: 15021.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria)
Plasmid details: Protein was expressed as fusion with N-terminal tag MGSSHHHHHHSSGRENLYFQGHM and C-terminal fusion of GS
Plasmid: modified peT15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X0E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.77 Å3/Da / Density % sol: 30.7 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Details: Zhang, R.G., (2001) Structure, 9, 1095.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
31.75 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,0.9791,0.95200
DetectorType: SBC-2 / Detector: CCD / Date: Nov 20, 2001 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.9521
ReflectionResolution: 1.4→50 Å / Num. all: 20453 / Num. obs: 19451 / % possible obs: 95.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.49 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.25
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.875 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.66 / Num. unique all: 1829 / % possible all: 87.7
Reflection
*PLUS
Lowest resolution: 50 Å

-
Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→20.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 485887.96 / Data cutoff high rms absF: 485887.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1571 5.2 %RANDOM
Rwork0.218 ---
obs0.218 19451 74.1 %-
all-20453 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9317 Å2 / ksol: 0.389531 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.1 Å
Refinement stepCycle: LAST / Resolution: 1.4→20.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 0 125 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.232 145 5.5 %
Rwork0.22 2482 -
obs--38.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 40 Å / Num. reflection obs: 19651 / σ(F): 0 / Rfactor Rfree: 0.2408 / Rfactor Rwork: 0.2094
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

+
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