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- PDB-2ixc: RmlC M. tuberculosis with dTDP-rhamnose -

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Basic information

Entry
Database: PDB / ID: 2ixc
TitleRmlC M. tuberculosis with dTDP-rhamnose
ComponentsDTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
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 / polysaccharide 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
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / 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: 1.79 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 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 RMLC
B: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
C: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
D: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5418
Polymers89,3484
Non-polymers2,1934
Water20,9331162
1
A: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
B: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7714
Polymers44,6742
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-22 kcal/mol
Surface area15880 Å2
MethodPISA
2
C: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
D: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7714
Polymers44,6742
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-23 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.778, 56.845, 90.700
Angle α, β, γ (deg.)89.90, 78.28, 82.33
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 5 - 190 / Label seq-ID: 5 - 190

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC / DTDP-4-KETO-6-DEOXYGLUCOSE 3 / 5-EPIMERASE / DTDP-L-RHAMNOSE SYNTHETASE / THYMIDINE DIPHOSPHO-4- ...DTDP-4-KETO-6-DEOXYGLUCOSE 3 / 5-EPIMERASE / DTDP-L-RHAMNOSE SYNTHETASE / THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3 / 5-EPIMERASE / DTDP-4-DEHYDRORHAMNOSE 3 / 5-EPIMERASE


Mass: 22336.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O06330, UniProt: P9WH11*PLUS, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.14 Å3/Da / Density % sol: 42.1 %
Crystal growDetails: 23% (w/v) polyethylene glycol (PEG) 8000, 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate (pH 5.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→36 Å / Num. obs: 84823 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.8 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→36.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.449 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3784 5 %RANDOM
Rwork0.151 ---
obs0.154 71906 92.6 %-
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: 25.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20.09 Å2-0.01 Å2
2--0.09 Å20.04 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.79→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 140 1162 7474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216480
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9668868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43623.117308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29515940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9511556
X-RAY DIFFRACTIONr_chiral_restr0.0920.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.23079
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24373
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21049
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.276
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.54077
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18626364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.82832793
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6444.52504
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.18736870
X-RAY DIFFRACTIONr_sphericity_free3.81431163
X-RAY DIFFRACTIONr_sphericity_bonded1.75736312
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Number: 1441 / Refine-ID: X-RAY DIFFRACTION

Ens-IDTypeRms dev position (Å)Weight position
1medium positional0.280.5
2medium positional0.410.5
3medium positional0.160.5
1medium thermal0.532
2medium thermal0.732
3medium thermal0.532
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 242 -
Rwork0.207 5105 -
obs--89.01 %

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