[English] 日本語
Yorodumi
- PDB-4nmy: Crystal Structure of the Thiamin-bound form of Substrate-binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nmy
TitleCrystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile
ComponentsABC-type transport system, extracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / SBP fold
Function / homology
Function and homology information


thiamine biosynthetic process
Similarity search - Function
NMT1/THI5 family / SsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-VIB / ABC-type transport system, extracellular solute-binding protein
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.896 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile
Authors: Kim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC-type transport system, extracellular solute-binding protein
B: ABC-type transport system, extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2564
Polymers68,7262
Non-polymers5312
Water7,548419
1
A: ABC-type transport system, extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6282
Polymers34,3631
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC-type transport system, extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6282
Polymers34,3631
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.529, 76.867, 154.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ABC-type transport system, extracellular solute-binding protein


Mass: 34362.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_19790 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q187U0
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN, VITAMIN B1


Mass: 265.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.2 M ammonium sulfate, 0.1 M sodium succinate pH7.5, 0.96 % LDAO, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 47478 / Num. obs: 47478 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 19.33 Å2 / Rsym value: 0.085 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2273 / Rsym value: 0.581 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.896→38.433 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2368 5.05 %random
Rwork0.164 ---
obs0.166 46934 98.25 %-
all-46934 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.25 Å2
Refinement stepCycle: LAST / Resolution: 1.896→38.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 36 419 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084918
X-RAY DIFFRACTIONf_angle_d1.0976662
X-RAY DIFFRACTIONf_dihedral_angle_d14.3761816
X-RAY DIFFRACTIONf_chiral_restr0.077718
X-RAY DIFFRACTIONf_plane_restr0.004848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8965-1.93520.26711180.2182089220780
1.9352-1.97720.27951550.212493264896
1.9772-2.02320.26311350.19722596273199
2.0232-2.07380.30291300.192619274999
2.0738-2.12990.2461440.187826102754100
2.1299-2.19260.22611320.17912640277299
2.1926-2.26330.24271560.17392607271399
2.2633-2.34420.19661260.173126592785100
2.3442-2.43810.21641400.172226152755100
2.4381-2.5490.21021240.167926692793100
2.549-2.68330.24841340.17126622796100
2.6833-2.85140.22971320.174426792811100
2.8514-3.07150.18011290.172426982827100
3.0715-3.38040.19911570.173326622819100
3.3804-3.86920.19321350.152727192854100
3.8692-4.87320.15151610.124527142875100
4.8732-38.44140.15321600.14152835299599

+
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