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- PDB-1dzt: RMLC FROM SALMONELLA TYPHIMURIUM -

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Basic information

Entry
Database: PDB / ID: 1dzt
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
3'-O-ACETYLTHYMIDINE-5'-DIPHOSPHATE / Chem-TPE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)42,89410
Polymers41,3692
Non-polymers1,5258
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-62.2 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.800, 71.800, 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: (0.04177, 0.79933, -0.59943), (0.79444, -0.39041, -0.46524), (-0.6059, -0.45678, -0.65133)
Vector: 3.30174, 55.73008, 79.9013)

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Components

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Protein , 1 types, 2 molecules AB

#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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P26394, dTDP-4-dehydrorhamnose 3,5-epimerase

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Non-polymers , 5 types, 327 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TPE / 3'-O-ACETYLTHYMIDINE-(5' DIPHOSPHATE PHENYL ESTER)


Mass: 520.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O12P2
#5: Chemical ChemComp-ATY / 3'-O-ACETYLTHYMIDINE-5'-DIPHOSPHATE


Mass: 444.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N2O12P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.32 Å3/Da / Density % sol: 62.93 %
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: SRS / Beamline: PX9.6 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 28562 / % possible obs: 99 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 30.7
Reflection
*PLUS
Lowest resolution: 3 Å / % possible obs: 98.9 % / Redundancy: 4.2 %
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZR

1dzr


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 -5 %RANDOM
Rwork0.232 ---
obs0.232 28562 99 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 96 319 3341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.71
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40 Å2
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0088

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