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- PDB-4j7h: Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP... -

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Basic information

Entry
Database: PDB / ID: 4j7h
TitleCrystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-benzene and dTDP-rhamnose
ComponentsEvaA 2,3-dehydratase
KeywordsBIOSYNTHETIC PROTEIN / Nudix hydrolase superfamily / dehydration
Function / homology
Function and homology information


dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase / antibiotic biosynthetic process / lyase activity
Similarity search - Function
EvaA sugar 2,3-dehydratase subunit / dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase / dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase superfamily / NDP-hexose 2,3-dehydratase / Nucleoside Triphosphate Pyrophosphohydrolase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-TLO / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHolden, H.M. / Kubiak, R.L. / Thoden, J.B.
CitationJournal: Biochemistry / Year: 2013
Title: Structure of EvaA: A Paradigm for Sugar 2,3-Dehydratases.
Authors: Kubiak, R.L. / Thoden, J.B. / Holden, H.M.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: EvaA 2,3-dehydratase
B: EvaA 2,3-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,42712
Polymers106,0022
Non-polymers2,42610
Water14,376798
1
A: EvaA 2,3-dehydratase
hetero molecules

A: EvaA 2,3-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,55114
Polymers106,0022
Non-polymers2,55012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8320 Å2
ΔGint4 kcal/mol
Surface area33760 Å2
MethodPISA
2
B: EvaA 2,3-dehydratase
hetero molecules

B: EvaA 2,3-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,30310
Polymers106,0022
Non-polymers2,3028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area8100 Å2
ΔGint1 kcal/mol
Surface area33820 Å2
MethodPISA
3
A: EvaA 2,3-dehydratase
hetero molecules

A: EvaA 2,3-dehydratase
hetero molecules

B: EvaA 2,3-dehydratase
hetero molecules

B: EvaA 2,3-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,85424
Polymers212,0034
Non-polymers4,85120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_445-x-1/2,y-1/2,-z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area17500 Å2
ΔGint-6 kcal/mol
Surface area66500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.681, 108.635, 110.133
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 EvaA 2,3-dehydratase / PCZA361.3


Mass: 53000.762 Da / Num. of mol.: 2 / Mutation: R381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: NRRL 18098 / Gene: EvaA / Plasmid: pET-28JT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O52793
#2: Chemical ChemComp-TLO / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine / thymidine diphosphate phenol


Mass: 478.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O11P2
#3: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 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: 1.69→110.13 Å / Num. all: 135159 / Num. obs: 135159 / % possible obs: 97.2 % / Redundancy: 7 % / Rsym value: 0.054 / Net I/σ(I): 55.7
Reflection shellResolution: 1.7→1.86 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 12455 / % possible all: 90.7

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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 / Resolution: 1.69→110.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.439 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19072 6793 5 %RANDOM
Rwork0.16468 ---
obs0.166 128340 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.69→110.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 0 156 798 8067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227539
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.96310307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08823.255384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.267151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3061574
X-RAY DIFFRACTIONr_chiral_restr0.1760.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215864
X-RAY DIFFRACTIONr_mcbond_it2.1381.54485
X-RAY DIFFRACTIONr_mcangle_it3.35327284
X-RAY DIFFRACTIONr_scbond_it4.39833054
X-RAY DIFFRACTIONr_scangle_it6.74.53011
LS refinement shellResolution: 1.694→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 422 -
Rwork0.202 8268 -
obs--85.3 %

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