[English] 日本語
Yorodumi
- PDB-1dak: DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION I... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1dak
TitleDETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE
ComponentsDETHIOBIOTIN SYNTHETASE
KeywordsLIGASE / PHOSHPORYL TRANSFER / BIOTIN BIOSYNTHESIS / KINETIC CRYSTALLOGRAPHY
Function / homologyDethiobiotin synthase BioD / P-loop containing nucleoside triphosphate hydrolase / CobQ/CobB/MinD/ParA nucleotide binding domain / dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol / ATP-dependent dethiobiotin synthetase BioD 1
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / 1.6 Å resolution
AuthorsKaeck, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Authors: Kack, H. / Gibson, K.J. / Lindqvist, Y. / Schneider, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 31, 1998 / Release: Apr 6, 1999
RevisionDateData content typeGroupProviderType
1.0Apr 6, 1999Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9116
Polyers24,0281
Non-polymers8835
Water3,891216
1
A: DETHIOBIOTIN SYNTHETASE
hetero molecules

A: DETHIOBIOTIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,82312
Polyers48,0572
Non-polymers1,76610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)6950
ΔGint (kcal/M)-106
Surface area (Å2)16690
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)72.680, 48.190, 61.070
Angle α, β, γ (deg.)90.00, 106.58, 90.00
Int Tables number5
Space group name H-MC 1 2 1

-
Components

-
Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide DETHIOBIOTIN SYNTHETASE


Mass: 24028.289 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Cellular location: CYTOPLASM / Genus (production host): Escherichia / Cellular location (production host): CYTOPLASM / Gene (production host): BIOD / Production host: Escherichia coli (E. coli) / References: UniProt: P13000, dethiobiotin synthase

-
Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#4: Chemical ChemComp-DPU / MIXED CARBAMIC PHOSPHORIC ACID ANHYDRIDE OF 7,8-DIAMINONONANIC ACID


Mass: 312.257 Da / Num. of mol.: 1 / Formula: C10H21N2O7P
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 / Density percent sol: 42.3 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Details: drop contained 0.003ml of protein solution mixed with 0.074ml of well solution.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
130 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
3100 mM1reservoirMgAc
49-12 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID09 / Synchrotron site: ESRF / Beamline: ID09 / Wavelength: 0.7606
DetectorType: PRINCETON 2K / Detector: CCD / Collection date: Oct 1, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7606 / Relative weight: 1
ReflectionD resolution high: 1.6 / D resolution low: 25 / Number obs: 86120 / Rsym value: 0.078 / NetI over sigmaI: 16 / Redundancy: 3.2 % / Percent possible obs: 99
Reflection shellHighest resolution: 1.6 / Lowest resolution: 1.66 / MeanI over sigI obs: 2.8 / Rsym value: 0.43 / Redundancy: 2.6 % / Percent possible all: 92.4
Reflection
*PLUS
Rmerge I obs: 0.078
Reflection shell
*PLUS
Percent possible obs: 92.4 / Rmerge I obs: 0.43

-
Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefineMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 13.6
Least-squares processR factor R free: 0.21 / R factor R work: 0.184 / Highest resolution: 1.6 / Lowest resolution: 20 / Number reflection R free: 1505 / Number reflection obs: 29418 / Percent reflection R free: 5.1 / Percent reflection obs: 99
Refine hist #LASTHighest resolution: 1.6 / Lowest resolution: 20
Number of atoms included #LASTProtein: 1692 / Nucleic acid: 0 / Ligand: 54 / Solvent: 216 / Total: 1962
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.020
X-RAY DIFFRACTIONp_angle_d0.0200.040
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8622.000
X-RAY DIFFRACTIONp_mcangle_it1.3353.000
X-RAY DIFFRACTIONp_scbond_it1.2272.000
X-RAY DIFFRACTIONp_scangle_it1.9493.000
X-RAY DIFFRACTIONp_plane_restr0.0165
X-RAY DIFFRACTIONp_chiral_restr0.0810.150
X-RAY DIFFRACTIONp_singtor_nbd0.1720.300
X-RAY DIFFRACTIONp_multtor_nbd0.2580.300
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.17.0
X-RAY DIFFRACTIONp_staggered_tor15.915.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.184

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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