[English] 日本語
Yorodumi
- PDB-6af2: Crystal structure of N-terminus deletion mutant of Mycobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6af2
TitleCrystal structure of N-terminus deletion mutant of Mycobacterium avium diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase
ComponentsHIT domain-containing protein
KeywordsTRANSFERASE / Nucleoside
Function / homology
Function and homology information


catalytic activity / nucleotide binding
Similarity search - Function
: / FHIT family / HIT domain / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SPERMINE / HIT domain-containing protein / HIT domain-containing protein
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å
AuthorsMori, S. / Honda, N. / Kim, H. / Rimbara, E. / Shibayama, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K07377 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Crystal structure of N-terminus deletion mutant of Mycobacterium avium diadenosine tetraphosphate phosphorylase
Authors: Mori, S. / Honda, N. / Kim, H. / Rimbara, E. / Shibayama, K.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIT domain-containing protein
B: HIT domain-containing protein
C: HIT domain-containing protein
D: HIT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,88611
Polymers86,5914
Non-polymers1,2967
Water2,252125
1
A: HIT domain-containing protein
C: HIT domain-containing protein
hetero molecules

B: HIT domain-containing protein
D: HIT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,88611
Polymers86,5914
Non-polymers1,2967
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area10980 Å2
ΔGint-57 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.025, 104.837, 111.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))
21(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))
31(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))
41(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLNGLN(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA4 - 520 - 21
12THRTHRTHRTHR(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA1329
13ILEILEILEILE(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA42 - 15058 - 166
14GLNGLNSERSER(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA159 - 176175 - 192
21GLUGLUGLNGLN(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB36 - 3752 - 53
22THRTHRTHRTHR(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB4056
23ILEILEILEILE(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB42 - 15058 - 166
24GLNGLNSERSER(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB159 - 176175 - 192
31GLUGLUGLNGLN(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC36 - 3752 - 53
32THRTHRTHRTHR(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC4056
33ILEILEILEILE(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC42 - 15058 - 166
34GLNGLNSERSER(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC159 - 176175 - 192
41GLUGLUGLNGLN(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD4 - 520 - 21
42THRTHRTHRTHR(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD1329
43ILEILEILEILE(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD42 - 15058 - 166
44GLNGLNSERSER(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD159 - 176175 - 192

-
Components

#1: Protein
HIT domain-containing protein / diadenosine 5' / 5'''-P1 / P4-tetraphosphate phosphorylase


Mass: 21647.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Gene: CKJ66_17020, CKJ75_15745 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2A2ZGT3, UniProt: Q73WE5*PLUS
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Hepes (pH 7.6), 0.2 M CaCl2, 28% PEG 400, 2mM spermine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16834 / % possible obs: 89.4 % / Redundancy: 9.5 % / Biso Wilson estimate: 44.97 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 485 / % possible all: 54

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANO

3ano


Resolution: 3.001→24.845 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.266 861 5.13 %
Rwork0.2076 --
obs0.2107 16776 89.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.98 Å2 / Biso mean: 38.554 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 3.001→24.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 88 125 4666
Biso mean--38.67 33.63 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114630
X-RAY DIFFRACTIONf_angle_d1.5496258
X-RAY DIFFRACTIONf_chiral_restr0.083702
X-RAY DIFFRACTIONf_plane_restr0.011799
X-RAY DIFFRACTIONf_dihedral_angle_d9.1452759
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2374X-RAY DIFFRACTION16.558TORSIONAL
12B2374X-RAY DIFFRACTION16.558TORSIONAL
13C2374X-RAY DIFFRACTION16.558TORSIONAL
14D2374X-RAY DIFFRACTION16.558TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0012-3.18890.3499830.21591745182860
3.1889-3.43450.28411160.21252447256383
3.4345-3.77910.30751500.19562846299697
3.7791-4.32340.23951680.18062881304998
4.3234-5.43770.24021490.18992950309998
5.4377-24.84590.25861950.24273046324199

+
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