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- PDB-2ixk: RmlC P aeruginosa with dTDP-4-keto rhamnnose (the product of the ... -

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Basic information

Entry
Database: PDB / ID: 2ixk
TitleRmlC P aeruginosa with dTDP-4-keto rhamnnose (the product of the reaction)
ComponentsDTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
KeywordsISOMERASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS / EPIMERISE / EPIMERASE / EPIMERIZE
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
DTDP-4-KETO-L-RHAMNOSE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, C. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Rmlc, a C3' and C5' Carbohydrate Epimerase, Appears to Operate Via an Intermediate with an Unusual Twist Boat Conformation.
Authors: Dong, C. / Major, L.L. / Srikannathasan, V. / Errey, J.C. / Giraud, M.F. / Lam, J.S. / Graninger, M. / Messner, P. / Mcneil, M.R. / Field, R.A. / Whitfield, C. / Naismith, J.H.
History
DepositionJul 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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)43,2904
Polymers42,1982
Non-polymers1,0932
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.378, 146.208, 44.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE / MLC / DTDP-4-KETO-6-DEOXY-D-GLUCOSE 3 / 5 EPIMERASE


Mass: 21098.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HU21
#2: Chemical ChemComp-TDO / DTDP-4-KETO-L-RHAMNOSE


Mass: 546.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N2O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsEXTRA SMS AT N-TERMINUS CLONING ARTEFACT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→21 Å / Num. obs: 40067 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.8 / % possible all: 40

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→72.55 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.934 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE OH OF TYR 134 IS SET AT ZERO OCCUPANCY BECAUSE WE ARE UNSURE WHETHER IT IS A CHEMICAL LINK WITH THE LIGAND.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2045 5.1 %RANDOM
Rwork0.15 ---
obs0.152 37930 84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---1 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 70 528 3580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223141
X-RAY DIFFRACTIONr_bond_other_d0.0010.022746
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9594266
X-RAY DIFFRACTIONr_angle_other_deg0.75136358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.10722.892166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55315486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7321530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.1990.2537
X-RAY DIFFRACTIONr_nbd_other0.1990.22732
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21485
X-RAY DIFFRACTIONr_nbtor_other0.0830.21840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2339
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3341.52365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49322938
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16531563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0894.51328
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 63
Rwork0.174 1326
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)
10.81890.129-0.16570.887-0.18650.50110.0031-0.0401-0.05370.068-0.00770.1279-0.0226-0.020.00460.00040.01720.009-0.00050.0011-0.004721.88413.13827.12
21.08290.4207-0.21810.82560.04030.653-0.03720.1250.0562-0.11120.0415-0.0506-0.05590.0406-0.00430.01040.0030.00780.00280.0111-0.024740.17724.4899.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 184
2X-RAY DIFFRACTION2B1 - 184

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