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- PDB-2ixj: RmlC P aeruginosa native -

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Basic information

Entry
Database: PDB / ID: 2ixj
TitleRmlC P aeruginosa native
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
S,R MESO-TARTARIC ACID / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 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 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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

Downloads & links

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Assembly

Deposited unit
A: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0831
Non-polymers1501
Water1,56787
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)42,4664
Polymers42,1662
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)57.833, 57.833, 161.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 21082.795 Da / Num. of mol.: 1
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-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA SMA 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: 3.04 Å3/Da / Density % sol: 59.24 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.53→41 Å / Num. obs: 9710 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZR

1dzr


Resolution: 2.54→40.39 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.86 / SU B: 16.252 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 485 5 %RANDOM
Rwork0.21 ---
obs0.213 9165 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.54→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 10 87 1587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9372088
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25822.89283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97415242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1231515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21021
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6031.5939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97921468
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4883689
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3944.5620
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: 2.54→2.6 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.447 28
Rwork0.319 603
Refinement TLS params.Method: refined / Origin x: 4.637 Å / Origin y: 41.239 Å / Origin z: 28.78 Å
111213212223313233
T-0.0503 Å2-0.0057 Å2-0.034 Å2--0.0292 Å20.0064 Å2--0.0447 Å2
L1.8544 °2-0.2174 °20.3031 °2-2.6211 °22.1146 °2--8.4442 °2
S0.0873 Å °0.0569 Å °-0.0037 Å °-0.155 Å °-0.2053 Å °0.1406 Å °0.2216 Å °-0.6999 Å °0.118 Å °

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