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- PDB-2w3x: Crystal structure of a bifunctional hotdog fold thioesterase in e... -

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Basic information

Entry
Database: PDB / ID: 2w3x
TitleCrystal structure of a bifunctional hotdog fold thioesterase in enediyne biosynthesis, CalE7
ComponentsCALE7
KeywordsHYDROLASE / HOTDOG FOLD / THIOESTERASE / ENEDIYNE BIOSYNTHESIS
Function / homology
Function and homology information


Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-JEF / PHOSPHATE ION / PYROPHOSPHATE 2- / CalE7
Similarity search - Component
Biological speciesMICROMONOSPORA ECHINOSPORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKotaka, M. / Kong, R. / Qureshi, I. / Ho, Q.S. / Sun, H. / Liew, C.W. / Goh, L.P. / Cheung, P. / Mu, Y. / Lescar, J. / Liang, Z.X.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and Catalytic Mechanism of the Thioesterase Cale7 in Enediyne Biosynthesis.
Authors: Kotaka, M. / Kong, R. / Qureshi, I. / Ho, Q.S. / Sun, H. / Liew, C.W. / Goh, L.P. / Cheung, P. / Mu, Y. / Lescar, J. / Liang, Z.X.
History
DepositionNov 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALE7
B: CALE7
C: CALE7
D: CALE7
E: CALE7
F: CALE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,25313
Polymers102,9296
Non-polymers1,3247
Water9,476526
1
A: CALE7
B: CALE7
hetero molecules

A: CALE7
B: CALE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,19510
Polymers68,6194
Non-polymers1,5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10870 Å2
ΔGint-77.3 kcal/mol
Surface area30650 Å2
MethodPQS
2
C: CALE7
D: CALE7
E: CALE7
F: CALE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1558
Polymers68,6194
Non-polymers5364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12700 Å2
ΔGint-59.1 kcal/mol
Surface area29160 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.950, 73.320, 124.410
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.8542, -0.0191, -0.5196), (-0.015, -0.9998, 0.012), (-0.5198, -0.0025, -0.8543)30.2737, -20.5148, 109.1485
2given(-0.3523, -0.6056, -0.7135), (-0.6154, -0.4245, 0.6641), (-0.7051, 0.6731, -0.2231)0.143, 6.2889, -5.327
3given(0.104, 0.0912, 0.9904), (0.0747, -0.9937, 0.0837), (0.9918, 0.0653, -0.1101)-44.4233, 48.8232, 46.6265
4given(-0.7781, 0.5674, -0.2694), (0.5439, 0.394, -0.7409), (-0.3143, -0.723, -0.6152)-48.2109, 43.638, 47.2021

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
CALE7


Mass: 17154.803 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROMONOSPORA ECHINOSPORA (bacteria) / Strain: CALICHENSIS / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KNG2

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Non-polymers , 5 types, 533 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsJEFFAMINE (JEF): ONLY A FRAGMENT OF JEFFAMINE IS SEEN IN THE STRUCTURE

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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: 2.29 Å3/Da / Density % sol: 46.2 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 NA HEPES PH7.0, 28% JEFFAMINE-M600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.072121
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072121 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 90879 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EGI

2egi


Resolution: 1.75→29.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2342525.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4553 5 %RANDOM
Rwork0.196 ---
obs0.196 90790 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.57 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.97 Å20 Å22.41 Å2
2--7.95 Å20 Å2
3----2.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 62 526 7599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.464
X-RAY DIFFRACTIONc_mcangle_it4.938
X-RAY DIFFRACTIONc_scbond_it6.148
X-RAY DIFFRACTIONc_scangle_it8.9912
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 742 4.9 %
Rwork0.296 14328 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL_POP.PARGOL_POP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5JEF_FRAG.PARJEF_FRAG.TOP

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