[English] 日本語
Yorodumi
- PDB-4ut4: Burkholderia pseudomallei heptokinase WcbL, D-mannose complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ut4
TitleBurkholderia pseudomallei heptokinase WcbL, D-mannose complex.
ComponentsPUTATIVE SUGAR KINASE
KeywordsTRANSFERASE / CAPSULAR POLYSACCHARIDE / DRUG DISCOVERY / HEPTOPYRANOSE
Function / homology
Function and homology information


kinase activity / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
D,D-heptose 7-phosphate kinase / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 ...D,D-heptose 7-phosphate kinase / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Sugar kinase
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsVivoli, M. / Isupov, M.N. / Nicholas, R. / Hill, A. / Scott, A. / Kosma, P. / Prior, J. / Harmer, N.J.
CitationJournal: Chem.Biol. / Year: 2015
Title: Unraveling the B.Pseudomallei Heptokinase Wcbl: From Structure to Drug Discovery.
Authors: Vivoli, M. / Isupov, M.N. / Nicholas, R. / Hill, A. / Scott, A.E. / Kosma, P. / Prior, J.L. / Harmer, N.J.
History
DepositionJul 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE SUGAR KINASE
B: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,33812
Polymers75,6952
Non-polymers64410
Water14,358797
1
A: PUTATIVE SUGAR KINASE
hetero molecules

A: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,33812
Polymers75,6952
Non-polymers64410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4760 Å2
ΔGint-98.7 kcal/mol
Surface area26130 Å2
MethodPISA
2
B: PUTATIVE SUGAR KINASE
hetero molecules

B: PUTATIVE SUGAR KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,33812
Polymers75,6952
Non-polymers64410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4860 Å2
ΔGint-97.7 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.100, 116.330, 168.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, -0.00023, 0.00336), (0.00023, -1, 0.00074), (0.00336, 0.00074, 0.99999)
Vector: -0.1344, -40.06847, 0.01523)

-
Components

#1: Protein PUTATIVE SUGAR KINASE / D-GLYCERO-BETA-D-MANNO-HEPTOSE-7-PHOSPHATE KINASE / WCBL


Mass: 37847.277 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI K96243 (bacteria)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: H7C745, EC: 2.7.1.167
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsD-MANNOSE (MAN): OBTAINED FROM SOAKING WITH 1.3 M OF D-MANNOSE AS CRYOPROTECTANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7 / Details: 0.5 M NACL, 10 MM HEPES PH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.94→69.48 Å / Num. obs: 73109 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.5
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
xia2data reduction
XDSdata reduction
Aimlessdata scaling
SHELXphasing
ARP/wARPphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.94→69.48 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.657 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23722 3714 5.1 %RANDOM
Rwork0.19334 ---
obs0.19552 69344 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---1.68 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.94→69.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 32 797 6135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195908
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9618094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58723.011269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.755151057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4221555
X-RAY DIFFRACTIONr_chiral_restr0.0840.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214529
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.776.8242913
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.85411.4013678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9917.8442991
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 266 -
Rwork0.281 5038 -
obs--99.05 %

+
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