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- PDB-2ixh: RmlC P aeruginosa with dTDP-rhamnose -

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Basic information

Entry
Database: PDB / ID: 2ixh
TitleRmlC P aeruginosa with dTDP-rhamnose
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
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.0Oct 26, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)43,2624
Polymers42,1662
Non-polymers1,0972
Water10,629590
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)43,2624
Polymers42,1662
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5590 Å2
ΔGint-20 kcal/mol
Surface area16210 Å2
MethodPISA
2
B: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
hetero molecules

B: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2624
Polymers42,1662
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area5300 Å2
ΔGint-19 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.915, 125.537, 109.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21A-2128-

HOH

31B-2045-

HOH

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Components

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


Mass: 21082.795 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-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA S AT N-TERMINUS CLONING ARTEFACT

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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: 2.19 Å3/Da / Density % sol: 43.3 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 30581 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→63.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.215 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1544 5.1 %RANDOM
Rwork0.19 ---
obs0.193 29011 99.9 %-
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: 28.35 Å2
Baniso -1Baniso -2Baniso -3
1-4.03 Å20 Å20 Å2
2---0.92 Å20 Å2
3----3.11 Å2
Refinement stepCycle: LAST / Resolution: 2→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 70 590 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223140
X-RAY DIFFRACTIONr_bond_other_d0.0010.022180
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9594266
X-RAY DIFFRACTIONr_angle_other_deg0.80835226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56622.892166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20615484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6921530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.1820.2482
X-RAY DIFFRACTIONr_nbd_other0.1810.22121
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21422
X-RAY DIFFRACTIONr_nbtor_other0.0770.21597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.288
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5481.52390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60922936
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.91731577
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3294.51330
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 92
Rwork0.245 2128
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)
11.25510.2110.61571.5895-0.45482.8857-0.10870.28860.0679-0.19020.0732-0.1256-0.10950.54030.0354-0.103-0.05460.01220.00050.00440.01249.561119.857816.7919
20.9441-0.38260.56851.21570.01695.38560.02980.07720.0382-0.243-0.18830.1577-0.9936-0.68680.1585-0.07040.1734-0.0545-0.1567-0.0284-0.124245.7869.641998.9419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 184
2X-RAY DIFFRACTION2B1 - 184

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