[English] 日本語
Yorodumi
- PDB-1rtv: RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal struc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rtv
TitleRmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / RmlC / main beta sheet structure
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / lipopolysaccharide biosynthetic process / polysaccharide biosynthetic 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
S,R MESO-TARTARIC ACID / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDong, C.J. / Naismith, J.H.
CitationJournal: TO BE PUBLISHED
Title: RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure
Authors: Dong, C.J. / Naismith, J.H.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0831
Non-polymers1501
Water36020
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4664
Polymers42,1662
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Unit cell
Length a, b, c (Å)57.833, 57.833, 161.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer.

-
Components

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


Mass: 21082.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: rmlc / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HU21, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium tartrate, 0.1M MOPS, 8% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: May 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40.4 Å / Num. all: 9732 / Num. obs: 9710 / % possible obs: 99.2 % / Observed criterion σ(F): 2.367 / Observed criterion σ(I): 1.8 / Redundancy: 7.3 % / Biso Wilson estimate: 56.26 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.088 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4 / Num. unique all: 1298 / Rsym value: 0.419 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DZR

1dzr


Resolution: 2.5→54.23 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.086 / SU ML: 0.315 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2.36 / σ(I): 1.8 / ESU R: 0.425 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28971 485 5 %RANDOM
Rwork0.23029 ---
all0.25 9710 --
obs0.23326 9166 95.17 %-
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: 30.642 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2--2.35 Å20 Å2
3----4.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 10 20 1520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211542
X-RAY DIFFRACTIONr_bond_other_d0.0010.021354
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9292087
X-RAY DIFFRACTIONr_angle_other_deg0.90533133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2723183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021751
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02359
X-RAY DIFFRACTIONr_nbd_refined0.2780.3316
X-RAY DIFFRACTIONr_nbd_other0.2560.31281
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1090.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.585
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2530.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7880.58
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1490.51
X-RAY DIFFRACTIONr_mcbond_it0.6421.5917
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23921467
X-RAY DIFFRACTIONr_scbond_it1.7963625
X-RAY DIFFRACTIONr_scangle_it3.0514.5620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 9 -
Rwork0.314 240 -
obs-1298 99.4 %
Refinement TLS params.Method: refined / Origin x: 4.482 Å / Origin y: 41.222 Å / Origin z: 28.744 Å
111213212223313233
T0.0107 Å20.0008 Å2-0.0251 Å2-0.0345 Å20.0092 Å2--0.0763 Å2
L1.2795 °2-0.1038 °20.1575 °2-2.0127 °21.7977 °2--6.9689 °2
S0.1131 Å °0.0928 Å °-0.0378 Å °-0.0978 Å °-0.1822 Å °0.1435 Å °0.2245 Å °-0.6409 Å °0.0691 Å °

+
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