[English] 日本語
Yorodumi
- PDB-2z0r: Crystal structure of hypothetical protein TTHA0547 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2z0r
TitleCrystal structure of hypothetical protein TTHA0547
ComponentsPutative uncharacterized protein TTHA0547
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha/beta protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyUncharacterised protein PF11572, DUF3234 / Protein of unknown function DUF3234 / Protein of unknown function (DUF3234) / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of hypothetical protein TTHA0547
Authors: Murayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein TTHA0547
B: Putative uncharacterized protein TTHA0547
C: Putative uncharacterized protein TTHA0547
D: Putative uncharacterized protein TTHA0547
E: Putative uncharacterized protein TTHA0547
F: Putative uncharacterized protein TTHA0547
G: Putative uncharacterized protein TTHA0547
H: Putative uncharacterized protein TTHA0547
I: Putative uncharacterized protein TTHA0547
J: Putative uncharacterized protein TTHA0547
K: Putative uncharacterized protein TTHA0547
L: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,64031
Polymers140,48212
Non-polymers1,15819
Water5,152286
1
A: Putative uncharacterized protein TTHA0547
B: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5454
Polymers23,4142
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
MethodPISA
2
C: Putative uncharacterized protein TTHA0547
D: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5815
Polymers23,4142
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
MethodPISA
3
E: Putative uncharacterized protein TTHA0547
F: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7127
Polymers23,4142
Non-polymers2985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
MethodPISA
4
G: Putative uncharacterized protein TTHA0547
H: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5815
Polymers23,4142
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
MethodPISA
5
I: Putative uncharacterized protein TTHA0547
J: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5454
Polymers23,4142
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
MethodPISA
6
K: Putative uncharacterized protein TTHA0547
L: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6776
Polymers23,4142
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
MethodPISA
7
A: Putative uncharacterized protein TTHA0547
B: Putative uncharacterized protein TTHA0547
C: Putative uncharacterized protein TTHA0547
D: Putative uncharacterized protein TTHA0547
E: Putative uncharacterized protein TTHA0547
F: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,83816
Polymers70,2416
Non-polymers59710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
MethodPISA
8
G: Putative uncharacterized protein TTHA0547
H: Putative uncharacterized protein TTHA0547
I: Putative uncharacterized protein TTHA0547
J: Putative uncharacterized protein TTHA0547
K: Putative uncharacterized protein TTHA0547
L: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,80215
Polymers70,2416
Non-polymers5629
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.501, 94.297, 101.734
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative uncharacterized protein TTHA0547


Mass: 11706.802 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKU6
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.45M Ammonium sulfate, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.97906, 0.97943, 0.964
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979061
20.979431
30.9641
ReflectionResolution: 2.3→42.84 Å / Num. obs: 56109 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.082 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.38 Å / % possible all: 97.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→42.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1572254.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2837 5.1 %RANDOM
Rwork0.229 ---
obs0.229 56087 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1099 Å2 / ksol: 0.359003 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.02 Å20 Å2-10.95 Å2
2---9.94 Å20 Å2
3---2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9303 0 51 286 9640
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 500 5.5 %
Rwork0.294 8606 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.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://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