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- PDB-1dzr: RmlC from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 1dzr
TitleRmlC from Salmonella typhimurium
ComponentsDTDP-4-DEHYDRORHAMNOSE 3\,5-EPIMERASE
KeywordsISOMERASE / 3\ / 5-HEXULOSE EPIMERASE
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / O antigen biosynthetic process / dTDP-rhamnose 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
dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.17 Å
AuthorsNaismith, J.H. / Giraud, M.F.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Rmlc, the Third Enzyme of Dtdp-L-Rhamnose Pathway, is a New Class of Epimerase.
Authors: Giraud, M.F. / Leonard, G.A. / Field, R.A. / Berlind, C. / Naismith, J.H.
History
DepositionMar 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DTDP-4-DEHYDRORHAMNOSE 3\,5-EPIMERASE
B: DTDP-4-DEHYDRORHAMNOSE 3\,5-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,21311
Polymers41,3692
Non-polymers8459
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-62 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.550, 71.550, 184.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.00951, 0.80109, -0.59847), (0.79061, -0.36042, -0.495), (-0.61224, -0.47787, -0.62992)
Vector: 4.20589, 55.35686, 79.99566)

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Components

#1: Protein DTDP-4-DEHYDRORHAMNOSE 3\,5-EPIMERASE / DTDP-4-KETO-6-DEOXYGLUCOSE 3\ / 5-EPIMERASE / DTDP-L-RHAMNOSE SYNTHETASE


Mass: 20684.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P26394, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7.75 / Method: vapor diffusion, sitting drop / Details: Giraud, M.-F., (1999) Acta Crystallogr, D55, 706.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMTris-HCl1drop
23.75 mg/mlprotein1drop
35 mMdithiothreitol1drop
41.6 Mammonium sulfate1reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.855, 0.9790, 0.9791
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8551
20.9791
30.97911
ReflectionResolution: 2.17→20 Å / Num. obs: 27292 / % possible obs: 92 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.046 / Rsym value: 0.047 / Net I/σ(I): 19.4
Reflection
*PLUS
% possible obs: 92.1 %
Reflection shell
*PLUS
Highest resolution: 2.17 Å / Lowest resolution: 2.21 Å / % possible obs: 80.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.17→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -5 %RANDOM
Rwork0.226 ---
obs0.226 27292 92 %-
Refinement stepCycle: LAST / Resolution: 2.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 50 281 3257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50 Å2

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