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Basic information

Entry
Database: PDB / ID: 1ofn
TitlePurification, crystallisation and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis; the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.
ComponentsPCZA361.16
KeywordsISOMERASE / EPIMERASE / VANCOMYCIN GROUP ANTIBIOTIC / EVAD
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose 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
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMerkel, A.B. / Naismith, J.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Purification, Crystallization and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatopsis Orientalis, the Fourth Enzyme in the Dtdp-L-Epivancosamine ...Title: Purification, Crystallization and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatopsis Orientalis, the Fourth Enzyme in the Dtdp-L-Epivancosamine Biosynthetic Pathway.
Authors: Merkel, A.B. / Temple, G.K. / Burkart, M.D. / Losey, H.C. / Beis, K. / Walsh, C.T. / Naismith, J.H.
History
DepositionApr 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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

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Assembly

Deposited unit
A: PCZA361.16
B: PCZA361.16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3926
Polymers45,0232
Non-polymers3684
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.575, 71.996, 57.100
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 PCZA361.16 / DTDP-4-KETO-6-DEOXY-GLUCOSE-5-EPIMERASE


Mass: 22511.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Strain: COSMID PCZA361(AJ223998) / Description: RECOMBINANT PROTEIN / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52806
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 25%PEG4K, 100MM MGCL2, 100MM TRIS-HCL, PH8.0, SITTING DROP,, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→57.735 Å / Num. obs: 65259 / % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZR

1dzr


Resolution: 1.5→57.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.979 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3334 5.1 %RANDOM
Rwork0.144 ---
obs0.146 62417 100 %-
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: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.62 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 24 543 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223207
X-RAY DIFFRACTIONr_bond_other_d0.0010.023010
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9724359
X-RAY DIFFRACTIONr_angle_other_deg0.75436958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3373402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94315567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023562
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02646
X-RAY DIFFRACTIONr_nbd_refined0.2260.3580
X-RAY DIFFRACTIONr_nbd_other0.1980.32835
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5418
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1760.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.440.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4020.536
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4461.52015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23123265
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.24331192
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9474.51094
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.22 239
Rwork0.171 4533

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