[English] 日本語
Yorodumi
- PDB-4wzy: Structure of mycobacterial maltokinase, the missing link in the e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wzy
TitleStructure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway (ATP complex)
ComponentsMaltokinase
KeywordsTRANSFERASE / Maltose / Glycogen / ATP
Function / homology
Function and homology information


maltokinase / trehalose biosynthetic process / carbohydrate phosphorylation / glycogen biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Maltokinase N-terminal cap domain / Maltokinase N-terminal cap domain / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphotransferase enzyme family / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Maltokinase
Similarity search - Component
Biological speciesMycobacterium vanbaalenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsFraga, J. / Empadinhas, N. / Pereira, P.J.B. / Macedo-Ribeiro, S.
CitationJournal: Sci Rep / Year: 2015
Title: Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway.
Authors: Fraga, J. / Maranha, A. / Mendes, V. / Pereira, P.J. / Empadinhas, N. / Macedo-Ribeiro, S.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2783
Polymers49,7471
Non-polymers5312
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-12 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.991, 73.767, 107.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21A-661-

HOH

31A-694-

HOH

41A-725-

HOH

51A-753-

HOH

61A-755-

HOH

-
Components

#1: Protein Maltokinase / MaK / Maltose-1-phosphate synthase


Mass: 49746.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium vanbaalenii (bacteria) / Strain: DSM 7251 / PYR-1 / Gene: mak, Mvan_5735 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1TH50, maltokinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Same as entry 4U98.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 54657 / % possible obs: 96.8 % / Redundancy: 4.7 % / Rsym value: 0.08 / Net I/σ(I): 10.7
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.72 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U94

4u94


Resolution: 1.71→47.903 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 2773 5.08 %
Rwork0.1766 --
obs0.178 54627 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→47.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 24 499 4003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073647
X-RAY DIFFRACTIONf_angle_d1.0364981
X-RAY DIFFRACTIONf_dihedral_angle_d11.9361341
X-RAY DIFFRACTIONf_chiral_restr0.043548
X-RAY DIFFRACTIONf_plane_restr0.005665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.73950.33891120.30042585X-RAY DIFFRACTION100
1.7395-1.77110.29931350.27072541X-RAY DIFFRACTION100
1.7711-1.80520.29471380.25882573X-RAY DIFFRACTION100
1.8052-1.84210.24851340.24082549X-RAY DIFFRACTION99
1.8421-1.88210.27711450.23732553X-RAY DIFFRACTION100
1.8821-1.92590.27111390.21862564X-RAY DIFFRACTION100
1.9259-1.97410.26781510.20882561X-RAY DIFFRACTION100
1.9741-2.02740.24511460.2042544X-RAY DIFFRACTION100
2.0274-2.08710.23941360.20092559X-RAY DIFFRACTION100
2.0871-2.15450.2061360.18542600X-RAY DIFFRACTION100
2.1545-2.23150.18871500.17552559X-RAY DIFFRACTION99
2.2315-2.32080.2241330.17112588X-RAY DIFFRACTION100
2.3208-2.42640.19051410.16762584X-RAY DIFFRACTION100
2.4264-2.55430.19851320.17542618X-RAY DIFFRACTION100
2.5543-2.71440.18411370.16852584X-RAY DIFFRACTION100
2.7144-2.92390.20461400.17332603X-RAY DIFFRACTION100
2.9239-3.21810.1991370.17212628X-RAY DIFFRACTION100
3.2181-3.68360.19481380.16272631X-RAY DIFFRACTION99
3.6836-4.64040.16091370.14022658X-RAY DIFFRACTION99
4.6404-47.92140.1891560.16362772X-RAY DIFFRACTION99
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)
12.0798-0.12630.40531.3506-0.62342.4315-0.00760.20540.3867-0.18310.03740.0119-0.2233-0.0733-0.0470.1604-0.01140.0230.17670.00430.227-65.414419.9747100.8739
21.37530.31960.35851.32040.63651.5110.0097-0.0324-0.01010.0378-0.0212-0.0755-0.0986-0.0160.00660.11440.012-0.00440.09330.01290.1019-38.993219.7431121.6711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 209 )
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 452 )

+
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