[English] 日本語
Yorodumi
- PDB-2uyt: Structure of L-rhamnulose kinase in complex with ADP and beta-L- ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uyt
TitleStructure of L-rhamnulose kinase in complex with ADP and beta-L- rhamnulose.
ComponentsRHAMNULOKINASE
KeywordsTRANSFERASE / RHAMNOSE DEGRADATION / IN-LINE PHOSPHORYL TRANSFER / HEXOKINASE-HSP70-ACTIN SUPERFAMILY / L-RHAMNULOSE KINASE / RHAMNOSE METABOLISM / KINASE / INDUCED FIT / RARE SUGARS
Function / homology
Function and homology information


rhamnulokinase / rhamnulokinase activity / rhamnose catabolic process / glycerol kinase activity / glycerol metabolic process / ATP binding / cytosol
Similarity search - Function
Rhamnulokinase / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 6-deoxy-beta-L-fructofuranose / Rhamnulokinase / Rhamnulokinase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGrueninger, D. / Schulz, G.E.
Citation
Journal: FEBS Lett. / Year: 2007
Title: Substrate Spectrum of L-Rhamnulose Kinase Related to Models Derived from Two Ternary Complex Structures.
Authors: Grueninger, D. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Structure and Reaction Mechanism of L-Rhamnulose Kinase from Escherichia Coli
Authors: Grueninger, D. / Schulz, G.E.
History
DepositionApr 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jul 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
Revision 1.4Dec 13, 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: RHAMNULOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5463
Polymers53,9551
Non-polymers5912
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.043, 51.093, 158.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RHAMNULOKINASE / L-RHAMNULOSE KINASE


Mass: 53954.715 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: Q8X899, UniProt: Q1R415*PLUS, rhamnulokinase
#2: Sugar ChemComp-LRH / 6-deoxy-beta-L-fructofuranose / 6-deoxy-beta-L-fructose / 6-deoxy-L-fructose / 6-deoxy-fructose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
b-L-6-deoxy-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 70 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 70 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 73 TO ALA
Sequence detailsTHE SEQUENCE DISCREPANCIES ARE BECAUSE THE DATABASE SEQUENCE IS FROM E.COLI STRAIN O157-H7. THE ...THE SEQUENCE DISCREPANCIES ARE BECAUSE THE DATABASE SEQUENCE IS FROM E.COLI STRAIN O157-H7. THE GENE WHICH WAS USED FOR PROTEIN EXPRESSION AND STRUCTURE DETERMINATION WAS ISOLATED FROM E.COLI BL21 (DE3).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 %
Crystal growDetails: 17% (W/V) PEG 8000, 0.12 M LICL, 20 MM ADP, 20 MM L-RHAMNULOSE-1-PHOSPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.55→80 Å / Num. obs: 60401 / % possible obs: 98.6 % / Observed criterion σ(I): 4.7 / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.2
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.7 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CGL

2cgl


Resolution: 1.55→79.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.162 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3021 5 %RANDOM
Rwork0.179 ---
obs0.181 57380 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.55→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 38 322 4067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213913
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9585360
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62824.368190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72715628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1451530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023030
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21910
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22706
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_refined0.2070.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6521.52489
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03223921
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65731615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5134.51427
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: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 186
Rwork0.224 3519
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)
11.17380.36170.83481.4190.62831.9923-0.0801-0.10060.131-0.06690.0483-0.0333-0.325-0.0310.03180.02380.025-0.0044-0.0273-0.0115-0.0108-12.89611.7827.377
20.6609-0.0610.30370.9539-0.04991.8573-0.00080.20620.0097-0.33370.0319-0.0752-0.15330.2027-0.0310.0788-0.01410.02190.03040.0003-0.0361-10.9621.8947.042
31.28860.23590.01740.7471-0.13731.61890.0149-0.0271-0.13-0.05670.031-0.0535-0.01350.1942-0.046-0.02780.0195-0.00130.0159-0.00590.0064-9.566-5.25822.315
42.0749-0.1961-0.20160.39010.4240.89720.0180.1162-0.1328-0.0597-0.09140.1161-0.0762-0.26190.0734-0.02410.0341-0.02510.082-0.00160.0353-37.277-5.18921.496
51.23830.1521-0.00750.6163-0.05090.8652-0.0106-0.1633-0.17270.02460.0207-0.02040.0858-0.006-0.0101-0.0190.021-0.00790.00140.02550.029-16.152-9.61930.459
65.31822.81881.25572.82010.21682.64230.0076-0.0995-0.41580.01450.18620.05430.3197-0.184-0.19380.0162-0.0259-0.00090.04790.06770.0757-28.092-17.49135.135
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 71
2X-RAY DIFFRACTION2A72 - 216
3X-RAY DIFFRACTION3A217 - 292
4X-RAY DIFFRACTION4A293 - 371
5X-RAY DIFFRACTION5A372 - 454
6X-RAY DIFFRACTION6A455 - 480

+
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