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- PDB-4hn1: Crystal Structure of H60N/Y130F double mutant of ChmJ, a 3'-monoe... -

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Basic information

Entry
Database: PDB / ID: 4hn1
TitleCrystal Structure of H60N/Y130F double mutant of ChmJ, a 3'-monoepimerase from Streptomyces bikiniensis in complex with dTDP
ComponentsPutative 3-epimerase in D-allose pathway
KeywordsUNKNOWN FUNCTION / 3'-monoepimerase / natural product / deoxysugar / chalcomycin / dTDP-mycinose / 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 / antibiotic biosynthetic process / carbohydrate metabolic process
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
THYMINE / THYMIDINE / THYMIDINE-5'-DIPHOSPHATE / dTDP-4-dehydro-6-deoxyglucose 3-epimerase
Similarity search - Component
Biological speciesStreptomyces bikiniensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _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)92,32423
Polymers89,2954
Non-polymers3,02819
Water7,548419
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)46,37113
Polymers44,6482
Non-polymers1,72311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-17 kcal/mol
Surface area16980 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)45,95310
Polymers44,6482
Non-polymers1,3058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-11 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.017, 141.017, 116.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 22323.840 Da / Num. of mol.: 4 / Mutation: H60N, Y130F
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

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Non-polymers , 5 types, 438 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#5: Chemical ChemComp-TDR / THYMINE / Thymine


Mass: 126.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3400, 2% 3-methyl-1,5-pentanediol, 100 mM MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→99.71 Å / Num. all: 143838 / Num. obs: 143838 / % possible obs: 96.1 % / Redundancy: 4.9 %
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.07 / Num. unique all: 13940 / Rsym value: 0.39 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HMZ

4hmz


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.074 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25373 7194 5 %RANDOM
Rwork0.21173 ---
obs0.21385 136644 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 196 419 6865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216672
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.9669124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96823.14328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76615956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721561
X-RAY DIFFRACTIONr_chiral_restr0.1780.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215257
X-RAY DIFFRACTIONr_mcbond_it2.0461.54019
X-RAY DIFFRACTIONr_mcangle_it3.19426475
X-RAY DIFFRACTIONr_scbond_it4.89132653
X-RAY DIFFRACTIONr_scangle_it7.5564.52637
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 493 -
Rwork0.334 9738 -
obs--92.58 %

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