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- PDB-4hmz: Crystal Structure of ChmJ, a 3'-monoepimerase from Streptomyces b... -

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Basic information

Entry
Database: PDB / ID: 4hmz
TitleCrystal Structure of ChmJ, a 3'-monoepimerase from Streptomyces bikiniensis in complex with dTDP-quinovose
ComponentsPutative 3-epimerase in D-allose pathway
KeywordsUNKNOWN FUNCTION / 3'-monoepimerase / natural product / deoxysugar / chalcomycin / dTDP-mycinose / dTDP-quinovose / Cupin fold / nucleotide-linked sugar / Epimerization
Function / homology
Function and homology information


dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / antibiotic 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
Chem-18T / dTDP-4-dehydro-6-deoxyglucose 3-epimerase
Similarity search - Component
Biological speciesStreptomyces bikiniensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHolden, H.M. / Kubiak, R.L.
CitationJournal: Biochemistry / Year: 2012
Title: Structural and Functional Studies on a 3'-Epimerase Involved in the Biosynthesis of dTDP-6-deoxy-d-allose.
Authors: Kubiak, R.L. / Phillips, R.K. / Zmudka, M.W. / Ahn, M.R. / Maka, E.M. / Pyeatt, G.L. / Roggensack, S.J. / Holden, H.M.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative 3-epimerase in D-allose pathway
B: Putative 3-epimerase in D-allose pathway
C: Putative 3-epimerase in D-allose pathway
D: Putative 3-epimerase in D-allose pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,53115
Polymers88,9034
Non-polymers2,62811
Water6,936385
1
A: Putative 3-epimerase in D-allose pathway
B: Putative 3-epimerase in D-allose pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7347
Polymers44,4512
Non-polymers1,2835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-3 kcal/mol
Surface area18270 Å2
MethodPISA
2
C: Putative 3-epimerase in D-allose pathway
D: Putative 3-epimerase in D-allose pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7968
Polymers44,4512
Non-polymers1,3456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint3 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.721, 140.721, 117.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Putative 3-epimerase in D-allose pathway


Mass: 22225.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces bikiniensis (bacteria) / Gene: chmJ / Plasmid: pET-31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q5SFD1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar
ChemComp-18T / [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate / dTDP-6-deoxy-d-allose


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


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3400, 2% 2-methyl-2,4-pentanediol, 100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 10, 2012 / Details: Montel
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99.5 Å / Num. all: 77282 / Num. obs: 73347 / % possible obs: 94.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.78 % / Mean I/σ(I) obs: 1.95 / Num. unique all: 9355 / Rsym value: 0.31 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C0Z

2c0z


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.194 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24883 3693 5 %RANDOM
Rwork0.19911 ---
obs0.20165 69652 94.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 168 385 6795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216665
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.9639123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63822.861332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52815959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5171565
X-RAY DIFFRACTIONr_chiral_restr0.1470.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215235
X-RAY DIFFRACTIONr_mcbond_it1.3661.54003
X-RAY DIFFRACTIONr_mcangle_it2.23326446
X-RAY DIFFRACTIONr_scbond_it3.65932662
X-RAY DIFFRACTIONr_scangle_it5.4684.52669
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 255 -
Rwork0.277 4706 -
obs--87.73 %

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