[English] 日本語
Yorodumi
- PDB-1pm7: RmlC (dTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pm7
TitleRmlC (dTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM MYCOBACTERIUM TUBERCULOSIS AND INHIBITOR DESIGN. THE APO STRUCTURE.
ComponentsRFBC
KeywordsISOMERASE / RmlC / Beta Barrel / main beta sheet structure / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / carbohydrate metabolic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDong, C. / Naismith, J.H. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: Novel inhibitors of an emerging target in Mycobacterium tuberculosis; substituted thiazolidinones as inhibitors of dTDP-rhamnose synthesis.
Authors: Babaoglu, K. / Page, M.A. / Jones, V.C. / McNeil, M.R. / Dong, C. / Naismith, J.H. / Lee, R.E.
History
DepositionJun 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RFBC
B: RFBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9766
Polymers44,6742
Non-polymers3024
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-10 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.066, 66.066, 87.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein RFBC / dTDP-4-dehydrorhamnose 3 / 5-epimerase / dTDP-6-deoxy-D-xylo-4-hexulose 3 / 5-epimerase


Mass: 22336.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rmlc (rfbc) / Plasmid: pET23b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O06330, UniProt: P9WH11*PLUS, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 8K, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.448 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2001
RadiationMonochromator: Liquid gallium cooled, bent, triangulary Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionResolution: 2.2→56.8 Å / Num. obs: 21690 / % possible obs: 99.9 % / Observed criterion σ(F): 8.73 / Observed criterion σ(I): 11 / Redundancy: 4 % / Biso Wilson estimate: 46.47 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.044 / Net I/σ(I): 1.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3149 / Rsym value: 0.364 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.261 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.8 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28339 1110 5.1 %RANDOM
Rwork0.2071 ---
obs0.21102 20551 99.84 %-
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: 24.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.254 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.2→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 20 155 3275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213196
X-RAY DIFFRACTIONr_bond_other_d0.0020.022826
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9344352
X-RAY DIFFRACTIONr_angle_other_deg0.90536538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2125396
X-RAY DIFFRACTIONr_chiral_restr0.1030.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023622
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02692
X-RAY DIFFRACTIONr_nbd_refined0.2190.2656
X-RAY DIFFRACTIONr_nbd_other0.2540.23305
X-RAY DIFFRACTIONr_nbtor_other0.0870.21934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.27
X-RAY DIFFRACTIONr_mcbond_it0.691.51988
X-RAY DIFFRACTIONr_mcangle_it1.06223198
X-RAY DIFFRACTIONr_scbond_it1.65631208
X-RAY DIFFRACTIONr_scangle_it2.3314.51154
X-RAY DIFFRACTIONr_rigid_bond_restr1.02723196
X-RAY DIFFRACTIONr_sphericity_free3.4722167
X-RAY DIFFRACTIONr_sphericity_bonded1.40123120
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.341 84
Rwork0.263 1511
obs-1511
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)
16.27162.35050.79392.9388-0.96925.30260.21710.41530.06910.3070.0011-0.085-0.82191.097-0.21810.2207-0.25640.05110.35-0.03460.1522.349128.4717-1.432
25.57262.6665-0.61383.92441.12955.19480.33370.1962-0.04660.3198-0.14340.08030.5249-1.2481-0.19030.0831-0.17320.00110.46230.04840.1497-2.764413.98921.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1991 - 199
2X-RAY DIFFRACTION2BB1 - 1991 - 199

+
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