[English] 日本語
Yorodumi
- PDB-5ukd: PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ukd
TitlePH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL TRANSFER TRANSITION STATE ANALOG
ComponentsURIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
KeywordsTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / NMP KINASE / PHOSPHORYL TRANSFER / TRANSITION STATE ANALOG COMPLEX
Function / homology
Function and homology information


pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CDP biosynthetic process / cytidylate kinase activity / phosphotransferase activity, phosphate group as acceptor / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / UMP kinase activity ...pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CDP biosynthetic process / cytidylate kinase activity / phosphotransferase activity, phosphate group as acceptor / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / UMP kinase activity / UDP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
UMP-CMP kinase / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / CYTIDINE-5'-MONOPHOSPHATE / UMP-CMP kinase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchlichting, I. / Reinstein, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
Authors: Schlichting, I. / Reinstein, J.
#1: Journal: Biochemistry / Year: 1997
Title: Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
Authors: Schlichting, I. / Reinstein, J.
#2: Journal: Biochemistry / Year: 1996
Title: Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: ...Title: Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.
Authors: Scheffzek, K. / Kliche, W. / Wiesmuller, L. / Reinstein, J.
#3: Journal: Febs Lett. / Year: 1995
Title: Crystallization and preliminary X-ray analysis of UMP/CMP-kinase from Dictyostelium discoideum with the specific bisubstrate inhibitor P1-(adenosine 5')-P5-(uridine 5')-pentaphosphate (UP5A).
Authors: Wiesmuller, L. / Scheffzek, K. / Kliche, W. / Goody, R.S. / Wittinghofer, A. / Reinstein, J.
#4: Journal: J.Biol.Chem. / Year: 1990
Title: cDNA-derived sequence of UMP-CMP kinase from Dictyostelium discoideum and expression of the enzyme in Escherichia coli.
Authors: Wiesmuller, L. / Noegel, A.A. / Barzu, O. / Gerisch, G. / Schleicher, M.
History
DepositionApr 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 12, 2014Group: Refinement description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.6Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8305
Polymers21,9711
Non-polymers8594
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.500, 77.500, 100.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE / UMP/CMP KINASE


Mass: 21970.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX2-214 / Gene: KCY_DICDI / Plasmid: PIMS5-CDUK-1 / Gene (production host): KCY_DICDI / Production host: Escherichia coli (E. coli) / References: UniProt: P20425, UMP/CMP kinase

-
Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsALF3 IS A PLANAR TRIGONAL TRANSITION STATE ANALOG OF THE PHOSPHORYL GROUP BEING TRANSFERRED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 65 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8.8 / Method: vapor diffusion, hanging drop / Details: Wiesmuller, L., (1995) FEBS Lett., 363, 22.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
214 %(w/v)PEG33501drop
350 mMTris-HCl1drop
4100 mM1dropMgCl2
50.02 %sodium azide1drop
610 mMDTE1drop
728 %(w/v)PEG33501reservoir
8100 mMTris-HCl1reservoir
9200 mM1reservoirMgCl2
100.04 %sodium azide1reservoir
1120 mMDTE1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 1, 1998 / Details: MIRRORS
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 33934 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.02 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 136455
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.31

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKD

3ukd


Rfactor Rfree: 0.241 / Rfactor Rwork: 0.209 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 53 181 1771
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor obs: 0.209 / Rfactor Rfree: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg0.7
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_deg1.5

+
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