[English] 日本語
Yorodumi
- PDB-3cq1: Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cq1
TitleStructure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (TT1362) from Thermus Thermophilus HB8
ComponentsPutative uncharacterized protein TTHB138
KeywordsOXIDOREDUCTASE / Thermus Thermophilus / DTDP-4-Keto-L-Rhamnose Reductase / Plasmid / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology: / Fe-S cluster assembly (FSCA) / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / MIP18 family-like domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJeyakanthan, J. / Satoh, S. / Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (TT1362) from Thermus Thermophilus HB8
Authors: Jeyakanthan, J. / Satoh, S. / Kitamura, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein TTHB138


Theoretical massNumber of molelcules
Total (without water)11,4951
Polymers11,4951
Non-polymers00
Water1,26170
1
A: Putative uncharacterized protein TTHB138

A: Putative uncharacterized protein TTHB138


Theoretical massNumber of molelcules
Total (without water)22,9902
Polymers22,9902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+1,z,y1
Buried area880 Å2
ΔGint-8.2 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.926, 121.926, 121.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

-
Components

#1: Protein Putative uncharacterized protein TTHB138 / DTDP-4-Keto-L-Rhamnose Reductase


Mass: 11495.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53W28
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.28 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Acetate, 12% PEG400, 0.1M Mg Chloride, pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 8, 2004 / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationMonochromator: SI 1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12570 / % possible obs: 100 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.08
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.344 / Num. unique all: 1246 / Rsym value: 0.361 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CU6

2cu6


Resolution: 1.9→49.78 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1574972.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 631 5.1 %RANDOM
Rwork0.207 ---
obs0.207 12285 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9839 Å2 / ksol: 0.376525 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms772 0 0 70 842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.226 73 5.1 %
Rwork0.206 1368 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.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