[English] 日本語
Yorodumi
- PDB-3o6w: Crystal structure of monomeric KlHxk1 in crystal form VIII (open ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o6w
TitleCrystal structure of monomeric KlHxk1 in crystal form VIII (open state)
ComponentsHexokinase
KeywordsTRANSFERASE / RNASEH-LIKE FOLD / HEXOKINASE / GLYCOLYSIS / GLUCOSE REPRESSION / ATP BINDING / MIG1 BINDING
Function / homology
Function and homology information


hexose metabolic process / hexokinase / fructokinase activity / glucokinase activity / glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding
Similarity search - Function
Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. ...Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hexokinase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKuettner, E.B. / Kettner, K. / Keim, A. / Kriegel, T.M. / Strater, N.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of Hexokinase KlHxk1 of Kluyveromyces lactis: A MOLECULAR BASIS FOR UNDERSTANDING THE CONTROL OF YEAST HEXOKINASE FUNCTIONS VIA COVALENT MODIFICATION AND OLIGOMERIZATION.
Authors: Kuettner, E.B. / Kettner, K. / Keim, A. / Svergun, D.I. / Volke, D. / Singer, D. / Hoffmann, R. / Muller, E.C. / Otto, A. / Kriegel, T.M. / Strater, N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and preliminary X-ray diffraction studies of hexokinase KlHxk1 from Kluyveromyces lactis
Authors: Kuettner, E.B. / Kriegel, T.M. / Keim, A. / Naumann, M. / Strater, N.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hexokinase
B: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,09010
Polymers107,3442
Non-polymers7458
Water11,349630
1
A: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9514
Polymers53,6721
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1386
Polymers53,6721
Non-polymers4665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.540, 93.590, 114.290
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hexokinase /


Mass: 53672.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: CBS2359/152 / Gene: KLLA0D11352g, RAG5 / Plasmid: pTSRAG5 / Production host: Kluyveromyces lactis (yeast) / Strain (production host): JA6-delta-rag5 / References: UniProt: P33284, hexokinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: 1microL reservoir + 1microL protein, reservoir: 2.4M di-ammonia phosphate, 0.1M Ches pH 9.6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 1mM xylose, 1mM ATP, ...Details: 1microL reservoir + 1microL protein, reservoir: 2.4M di-ammonia phosphate, 0.1M Ches pH 9.6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 1mM xylose, 1mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2009
Details: 1st mirror: Silicon, active surface 50 nm Rh-coated; 2nd mirror: Glas, active surface 50 nm Rh-coated
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 172567 / Num. obs: 171952 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.031 / Net I/σ(I): 21.7
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 12664 / Rsym value: 0.491 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O08

3o08


Resolution: 1.48→29.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.597 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FULL B FACTORS AND ANISO RECORDS WERE COMPUTED BY CCP4 PROGRAMM TLSANL
RfactorNum. reflection% reflectionSelection details
Rfree0.18391 1723 1 %RANDOM
Rwork0.16712 ---
obs0.1673 170225 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.67 Å2
2--1.08 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7269 0 45 630 7944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.98110168
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.545933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27425.315333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.524151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2471531
X-RAY DIFFRACTIONr_chiral_restr0.0950.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215603
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_it1.27234633
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1247510
X-RAY DIFFRACTIONr_scbond_it3.54862880
X-RAY DIFFRACTIONr_scangle_it5.85992655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 129 -
Rwork0.264 12500 -
obs--99.81 %
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)
10.60010.09830.28750.72590.28212.10710.0438-0.0134-0.0210.0044-0.0207-0.0043-0.0339-0.0294-0.02310.01980.00080.00980.0021-0.00470.05356.18995.366717.831
22.15690.06210.08441.6028-0.00271.54640.0366-0.0193-0.17840.0923-0.0278-0.19130.09970.164-0.00880.07640.0065-0.00530.0738-0.0430.077619.0435-11.3529-4.6582
31.09140.12230.00941.02760.04012.46540.01450.09540.0262-0.24540.00370.0810.0150.1134-0.01820.06160.0037-0.01090.0582-0.00020.068518.3094-15.5909-58.443
42.41360.225-0.2631.69860.04750.979-0.01270.07630.1481-0.09240.08650.1507-0.041-0.012-0.07380.0279-0.0260.00330.06430.00050.03730.9439-10.8974-33.4426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION1A210 - 456
3X-RAY DIFFRACTION2A77 - 209
4X-RAY DIFFRACTION2A457 - 485
5X-RAY DIFFRACTION3B2 - 76
6X-RAY DIFFRACTION3B210 - 456
7X-RAY DIFFRACTION4B77 - 209
8X-RAY DIFFRACTION4B457 - 485

+
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