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- PDB-1pm7: RmlC (dTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM... -

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Basic information

Entry
Database: PDB / ID: 1pm7
TitleRmlC (dTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM MYCOBACTERIUM TUBERCULOSIS AND INHIBITOR DESIGN. THE APO STRUCTURE.
ComponentsRFBC
KeywordsISOMERASE / RmlC / Beta Barrel / main beta sheet structure / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / : / carbohydrate metabolic 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
ACETATE ION / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDong, C. / Naismith, J.H. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: Novel inhibitors of an emerging target in Mycobacterium tuberculosis; substituted thiazolidinones as inhibitors of dTDP-rhamnose synthesis.
Authors: Babaoglu, K. / Page, M.A. / Jones, V.C. / McNeil, M.R. / Dong, C. / Naismith, J.H. / Lee, R.E.
History
DepositionJun 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RFBC
B: RFBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9766
Polymers44,6742
Non-polymers3024
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-10 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.066, 66.066, 87.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 22336.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rmlc (rfbc) / Plasmid: pET23b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O06330, UniProt: P9WH11*PLUS, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 8K, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.448 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2001
RadiationMonochromator: Liquid gallium cooled, bent, triangulary Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionResolution: 2.2→56.8 Å / Num. obs: 21690 / % possible obs: 99.9 % / Observed criterion σ(F): 8.73 / Observed criterion σ(I): 11 / Redundancy: 4 % / Biso Wilson estimate: 46.47 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.044 / Net I/σ(I): 1.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3149 / Rsym value: 0.364 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.261 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.8 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28339 1110 5.1 %RANDOM
Rwork0.2071 ---
obs0.21102 20551 99.84 %-
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: 24.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.254 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.2→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 20 155 3275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213196
X-RAY DIFFRACTIONr_bond_other_d0.0020.022826
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9344352
X-RAY DIFFRACTIONr_angle_other_deg0.90536538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2125396
X-RAY DIFFRACTIONr_chiral_restr0.1030.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023622
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02692
X-RAY DIFFRACTIONr_nbd_refined0.2190.2656
X-RAY DIFFRACTIONr_nbd_other0.2540.23305
X-RAY DIFFRACTIONr_nbtor_other0.0870.21934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.27
X-RAY DIFFRACTIONr_mcbond_it0.691.51988
X-RAY DIFFRACTIONr_mcangle_it1.06223198
X-RAY DIFFRACTIONr_scbond_it1.65631208
X-RAY DIFFRACTIONr_scangle_it2.3314.51154
X-RAY DIFFRACTIONr_rigid_bond_restr1.02723196
X-RAY DIFFRACTIONr_sphericity_free3.4722167
X-RAY DIFFRACTIONr_sphericity_bonded1.40123120
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.341 84
Rwork0.263 1511
obs-1511
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)
16.27162.35050.79392.9388-0.96925.30260.21710.41530.06910.3070.0011-0.085-0.82191.097-0.21810.2207-0.25640.05110.35-0.03460.1522.349128.4717-1.432
25.57262.6665-0.61383.92441.12955.19480.33370.1962-0.04660.3198-0.14340.08030.5249-1.2481-0.19030.0831-0.17320.00110.46230.04840.1497-2.764413.98921.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1991 - 199
2X-RAY DIFFRACTION2BB1 - 1991 - 199

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