[English] 日本語
Yorodumi
- PDB-2itm: Crystal structure of the E. coli xylulose kinase complexed with x... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2itm
TitleCrystal structure of the E. coli xylulose kinase complexed with xylulose
ComponentsXylulose kinase
KeywordsTRANSFERASE / xylulokinase / xylulose / kinase / ATPase / FGGY kinase
Function / homology
Function and homology information


1-deoxy-D-xylulose kinase activity / xylulokinase / xylulose catabolic process / D-xylulokinase activity / D-xylose catabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / protein homodimerization activity / ATP binding
Similarity search - Function
Xylulokinase / : / FGGY family of carbohydrate kinases signature 1. / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / 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 ...Xylulokinase / : / FGGY family of carbohydrate kinases signature 1. / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / 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
AMMONIUM ION / D-XYLULOSE / Xylulose kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
Authorsdi Luccio, E. / Voegtli, J. / Wilson, D.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli.
Authors: Di Luccio, E. / Petschacher, B. / Voegtli, J. / Chou, H.T. / Stahlberg, H. / Nidetzky, B. / Wilson, D.K.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 21, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Xylulose kinase
B: Xylulose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,04718
Polymers105,3382
Non-polymers70916
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-28 kcal/mol
Surface area36590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.883, 112.605, 143.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLNGLNAA1 - 761 - 76
21METMETGLNGLNBB1 - 761 - 76
32METMETLEULEUAA77 - 15077 - 150
42METMETLEULEUBB77 - 15077 - 150
53LEULEUMETMETAA151 - 160151 - 160
63LEULEUMETMETBB151 - 160151 - 160
74THRTHRTHRTHRAA161 - 224161 - 224
84THRTHRTHRTHRBB161 - 224161 - 224
95VALVALGLYGLYAA225 - 242225 - 242
105VALVALGLYGLYBB225 - 242225 - 242
116METMETTRPTRPAA243 - 300243 - 300
126METMETTRPTRPBB243 - 300243 - 300
137ALAALAASNASNAA301 - 359301 - 359
147ALAALAASNASNBB301 - 359301 - 359
158GLUGLUTHRTHRAA360 - 418360 - 418
168GLUGLUTHRTHRBB360 - 418360 - 418
179GLYGLYALAALAAA419 - 484419 - 484
189GLYGLYALAALABB419 - 484419 - 484

-
Components

#1: Protein Xylulose kinase / Xylulokinase


Mass: 52669.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xylB / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P09099, xylulokinase
#2: Sugar ChemComp-XUL / D-XYLULOSE


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 298 K / pH: 6
Details: Drops containing equal volume of 26 mg/ml protein solution and precipitant solution comprising of 1.5 M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, suspended over a 1 ml ...Details: Drops containing equal volume of 26 mg/ml protein solution and precipitant solution comprising of 1.5 M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, suspended over a 1 ml reservoir containing the precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2004
RadiationMonochromator: VERTICAL FOCUSING MIRROR SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→29.85 Å / Num. obs: 58656 / % possible obs: 96.4 % / Observed criterion σ(I): 1
Reflection scaleGroup code: 1
Reflection shellResolution: 2.1→30 Å / % possible all: 89.88

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→29.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.563 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2278 4 %RANDOM
Rwork0.201 ---
obs0.204 56530 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---2.27 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 42 431 7730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227440
X-RAY DIFFRACTIONr_bond_other_d00.024969
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.96410113
X-RAY DIFFRACTIONr_angle_other_deg4.313312129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0565947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.14124.214318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.822151206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.71548
X-RAY DIFFRACTIONr_chiral_restr0.340.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028345
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021439
X-RAY DIFFRACTIONr_nbd_refined0.2860.21982
X-RAY DIFFRACTIONr_nbd_other0.3130.25524
X-RAY DIFFRACTIONr_nbtor_refined0.2010.23615
X-RAY DIFFRACTIONr_nbtor_other0.1190.24098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2560.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.246
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.4821.55876
X-RAY DIFFRACTIONr_mcbond_other4.0741.51929
X-RAY DIFFRACTIONr_mcangle_it9.3527520
X-RAY DIFFRACTIONr_scbond_it13.833081
X-RAY DIFFRACTIONr_scangle_it15.2794.52593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2782tight positional0.710.05
3316loose positional0.925
2782tight thermal3.950.5
3316loose thermal7.1210
LS refinement shellResolution: 2.1→2.21 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 296 -
Rwork0.267 7313 -
obs--89.88 %

+
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