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- PDB-2c0z: The 1.6 A resolution crystal structure of NovW: a 4-keto-6-deoxy ... -

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Basic information

Entry
Database: PDB / ID: 2c0z
TitleThe 1.6 A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides
ComponentsNOVW
KeywordsISOMERASE / EPIMERASE / ANTIBIOTIC BIOSYNTHESIS / RMLC-LIKE CUPIN
Function / homology
Function and homology information


novobiocin biosynthetic process / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / isomerase activity / 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
dTDP-4-dehydrorhamnose 3-epimerase
Similarity search - Component
Biological speciesSTREPTOMYCES NIVEUS NCIMB 11891 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJakimowicz, P. / Tello, M. / Freel-Meyers, C.L. / Walsh, C.T. / Buttner, M.J. / Field, R.A. / Lawson, D.M.
Citation
Journal: Proteins / Year: 2006
Title: The 1.6 A Resolution Crystal Structure of Novw: A 4-Keto-6-Deoxy Sugar Epimerase from the Novobiocin Biosynthetic Gene Cluster of Streptomyces Spheroides
Authors: Jakimowicz, P. / Tello, M. / Freel-Meyers, C.L. / Walsh, C.T. / Buttner, M.J. / Field, R.A. / Lawson, D.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Studies on the Putative Dtdp Sugar Epimerase Novw from the Novobiocin Biosynthetic Cluster of Streptomyces Spheroides
Authors: Jakimowicz, P. / Freel-Meyers, C.L. / Walsh, C.T. / Buttner, M.J. / Lawson, D.M.
History
DepositionSep 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Mar 12, 2014Group: Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: NOVW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4865
Polymers23,2041
Non-polymers2824
Water3,603200
1
A: NOVW
hetero molecules

A: NOVW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,97310
Polymers46,4082
Non-polymers5658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area4530 Å2
ΔGint-33.4 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.354, 59.354, 109.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NOVW


Mass: 23204.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES NIVEUS NCIMB 11891 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9L9E5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES -8 TO 0 ARE THE EXPRESSION SYSTEM HIS-TAG

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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 Å3/Da / Density % sol: 36.7 %
Crystal growpH: 8.5
Details: 25% SATURATED AMMONIUM SULFATE IN 100MM TRIS-HCL PH8.5, pH 8.50

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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 / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→39 Å / Num. obs: 26449 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.7
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EP0

1ep0


Resolution: 1.6→51.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.241 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1348 5.1 %RANDOM
Rwork0.15 ---
obs0.152 25098 99.9 %-
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: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 17 200 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211574
X-RAY DIFFRACTIONr_bond_other_d0.0020.021424
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9612150
X-RAY DIFFRACTIONr_angle_other_deg1.5433287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021757
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02324
X-RAY DIFFRACTIONr_nbd_refined0.2450.2269
X-RAY DIFFRACTIONr_nbd_other0.2580.21590
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.2958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3480.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2141.5993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96421603
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7743581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3794.5547
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 91
Rwork0.153 1818

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