[English] 日本語
Yorodumi
- PDB-3fgn: Crystal structure of dethiobiotin synthetase in Mycobacterium tub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fgn
TitleCrystal structure of dethiobiotin synthetase in Mycobacterium tuberculosis
ComponentsDethiobiotin synthetase
KeywordsLIGASE / dethiobiotin synthetase / biotin biosynthesis / bioD / ATP-binding / Magnesium / Nucleotide-binding
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent dethiobiotin synthetase BioD / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.85 Å
AuthorsDey, S. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 2010
Title: Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
Authors: Dey, S. / Lane, J.M. / Lee, R.E. / Rubin, E.J. / Sacchettini, J.C.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dethiobiotin synthetase
B: Dethiobiotin synthetase
C: Dethiobiotin synthetase
D: Dethiobiotin synthetase


Theoretical massNumber of molelcules
Total (without water)101,2644
Polymers101,2644
Non-polymers00
Water5,765320
1
A: Dethiobiotin synthetase
B: Dethiobiotin synthetase


Theoretical massNumber of molelcules
Total (without water)50,6322
Polymers50,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area17630 Å2
MethodPISA
2
C: Dethiobiotin synthetase
D: Dethiobiotin synthetase


Theoretical massNumber of molelcules
Total (without water)50,6322
Polymers50,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-14 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.383, 104.684, 151.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Dethiobiotin synthetase / Dethiobiotin synthase / DTB synthetase / DTBS


Mass: 25315.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bioD, MT1621, MTCY336.33c, Rv1570 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O06620, UniProt: P9WPQ5*PLUS, dethiobiotin synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M sodium citrate, 0.1M imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.85→31.7 Å / Num. obs: 73740 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
SHARPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→31.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.527 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: SAD (SAMARIUM) USED FOR STRUCTURE DETERMINATION
RfactorNum. reflection% reflectionSelection details
Rfree0.25332 3705 5 %RANDOM
Rwork0.21436 ---
obs0.21632 70111 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--0.8 Å20 Å2
3----2.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 0 320 6638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226407
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9788763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97923.317205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12715933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8811553
X-RAY DIFFRACTIONr_chiral_restr0.0870.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.32914
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.54389
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5592
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.373
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.29554570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19677077
X-RAY DIFFRACTIONr_scbond_it4.58892008
X-RAY DIFFRACTIONr_scangle_it6.161111686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.523 190 -
Rwork0.446 3858 -
obs--73.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64240.47760.19130.35810.1950.987-0.0079-0.0523-0.06660.0153-0.0146-0.0496-0.0256-0.03940.0225-0.09130.02720.0026-0.0665-0.0198-0.0986-8.948427.5628-16.429
20.74880.5448-0.28090.43860.0251.351-0.0237-0.0351-0.05360.03270.01280.05070.09990.10350.0108-0.07260.01230.0068-0.0962-0.0177-0.11184.612217.1703-42.6046
32.15410.17120.00290.86190.39441.2490.00470.05280.0594-0.0252-0.06760.0252-0.1093-0.08930.0629-0.06770.0481-0.0144-0.1402-0.0241-0.1498-28.6497-4.8633-22.6574
40.1278-0.0949-0.27820.5367-0.2182.26230.10330.01280.05090.0058-0.1035-0.07620.18280.24410.00020.03910.0368-0.01370.03960.0311-0.0382-16.6625-7.0786.6339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 226
2X-RAY DIFFRACTION2B1 - 225
3X-RAY DIFFRACTION3C1 - 226
4X-RAY DIFFRACTION4D2 - 225

+
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