[English] 日本語
Yorodumi
- PDB-4bga: Nucleotide-bound open form of a putative sugar kinase MK0840 from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bga
TitleNucleotide-bound open form of a putative sugar kinase MK0840 from Methanopyrus kandleri
ComponentsPREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
KeywordsTRANSFERASE / ASKHA SUPERFAMILY / PHOSPHOTRANSFER / PSEUDOMUREIN
Function / homology
Function and homology information


amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / metallopeptidase activity / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #430 / Anhydro-N-acetylmuramic acid kinase / Anhydro-N-acetylmuramic acid kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / ADENOSINE-5'-DIPHOSPHATE / beta-D-glucopyranose / : / Predicted molecular chaperone distantly related to HSP70-fold metalloproteases
Similarity search - Component
Biological speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchacherl, M. / Baumann, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 from Methanopyrus Kandleri
Authors: Schacherl, M. / Waltersperger, S.M. / Baumann, U.
History
DepositionMar 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
B: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
C: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
D: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,73825
Polymers140,2394
Non-polymers3,50021
Water3,999222
1
A: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
C: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,85712
Polymers70,1192
Non-polymers1,73810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7.1 kcal/mol
Surface area31970 Å2
MethodPISA
2
B: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
D: PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,88113
Polymers70,1192
Non-polymers1,76211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-45.9 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.570, 111.670, 87.880
Angle α, β, γ (deg.)90.00, 89.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES / PUTATIVE SUGAR KINASE MK0840


Mass: 35059.656 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOPYRUS KANDLERI (archaea) / Strain: AV19 / Description: DSM6324 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TX37

-
Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 237 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsSUCROSE (SUC): CRYOPROTECTANT
Sequence detailsTRUNCATED CONSTRUCT LACKING THE FIRST 36 AMINO ACIDS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.24 % / Description: NONE
Crystal growpH: 7.5
Details: MIXED WITH 5 MM ADP, 10 MM MACL2, CRYSTALLIZED IN 0.2 M POTASSIUM SODIUM TARTRATE AND 20% PEG 3350, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→73.6 Å / Num. obs: 54893 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 7.6 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.95
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 7.69 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.98 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BG8 CHAIN A

4bg8


Resolution: 2.6→73.568 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 20.53 / Stereochemistry target values: ML
Details: FIRST 36 AMINO ACIDS OF THE PROTEIN ARE MISSING.GSH OVERHANG FROM THROMBIN-DIGESTED 6X-HIS TAG.
RfactorNum. reflection% reflection
Rfree0.208 2188 5 %
Rwork0.1542 --
obs0.1569 43757 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→73.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9611 0 213 222 10046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610011
X-RAY DIFFRACTIONf_angle_d1.18113642
X-RAY DIFFRACTIONf_dihedral_angle_d20.3793816
X-RAY DIFFRACTIONf_chiral_restr0.0651561
X-RAY DIFFRACTIONf_plane_restr0.0051799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65650.24961360.17732582X-RAY DIFFRACTION100
2.6565-2.71830.24661370.1782605X-RAY DIFFRACTION100
2.7183-2.78630.28871350.17722567X-RAY DIFFRACTION100
2.7863-2.86170.23351360.18422589X-RAY DIFFRACTION100
2.8617-2.94590.27741360.17842590X-RAY DIFFRACTION100
2.9459-3.0410.25111360.19032569X-RAY DIFFRACTION100
3.041-3.14960.28891360.18222592X-RAY DIFFRACTION100
3.1496-3.27570.24061360.17622592X-RAY DIFFRACTION100
3.2757-3.42480.19631360.16062585X-RAY DIFFRACTION100
3.4248-3.60540.22351370.15172602X-RAY DIFFRACTION100
3.6054-3.83130.20561370.14232602X-RAY DIFFRACTION100
3.8313-4.12710.16531370.13262600X-RAY DIFFRACTION100
4.1271-4.54230.15511370.11532595X-RAY DIFFRACTION100
4.5423-5.19950.15131380.12022617X-RAY DIFFRACTION100
5.1995-6.55010.20651380.15672622X-RAY DIFFRACTION100
6.5501-73.59720.19461400.16542660X-RAY DIFFRACTION100

+
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