3MCQ | pdb_00003mcq

Crystal structure of Thiamine-monophosphate kinase (Mfla_0573) from METHYLOBACILLUS FLAGELLATUS KT at 1.91 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.228 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of Thiamine-monophosphate kinase (Mfla_0573) from METHYLOBACILLUS FLAGELLATUS KT at 1.91 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 35.65 kDa 
  • Atom Count: 2,534 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 319 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiamine-monophosphate kinase319Methylobacillus flagellatus KTMutation(s): 0 
Gene Names: Mfla_0573
EC: 2.7.4.16
UniProt
Find proteins for Q1H3U4 (Methylobacillus flagellatus (strain ATCC 51484 / DSM 6875 / VKM B-1610 / KT))
Explore Q1H3U4 
Go to UniProtKB:  Q1H3U4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1H3U4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE


Download:Ideal Coordinates CCD File
K [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4

Query on PG4


Download:Ideal Coordinates CCD File
J [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.228 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.225α = 90
b = 59.225β = 90
c = 159.766γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-27
    Changes: Data collection, Structure summary