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- PDB-2xem: Induced-fit and allosteric effects upon polyene binding revealed ... -

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Basic information

Entry
Database: PDB / ID: 2xem
TitleInduced-fit and allosteric effects upon polyene binding revealed by crystal structures of the Dynemicin thioesterase
ComponentsDYNE7
KeywordsBIOSYNTHETIC PROTEIN / POLYKETIDE BIOSYNTHESIS / ENEDIYNE ANTITUMOR AGENT / THIOESTERASE
Function / homologyThioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Chem-SSV / DynE7
Function and homology information
Biological speciesMICROMONOSPORA CHERSINA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiew, C.W. / Sharff, A. / Kotaka, M. / Kong, R. / Bricogne, G. / Liang, Z.X. / Lescar, J.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Induced-Fit Upon Ligand Binding Revealed by Crystal Structures of the Hot-Dog Fold Thioesterase in Dynemicin Biosynthesis.
Authors: Liew, C.W. / Sharff, A. / Kotaka, M. / Kong, R. / Sun, H. / Qureshi, I. / Bricogne, G. / Liang, Z.X. / Lescar, J.
#1: Journal: 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.
History
DepositionMay 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: DYNE7
B: DYNE7
C: DYNE7
D: DYNE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9635
Polymers67,7494
Non-polymers2141
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-60.3 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.471, 65.387, 94.411
Angle α, β, γ (deg.)90.00, 99.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DYNE7 / TEBC


Mass: 16937.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROMONOSPORA CHERSINA (bacteria) / Plasmid: PCDF-2 LIC/EK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84HI7
#2: Chemical ChemComp-SSV / (3E,5E,7E,9E,11E,13E)-pentadeca-3,5,7,9,11,13-hexaen-2-one


Mass: 214.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5 / Details: PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 39917 / % possible obs: 97.3 % / Observed criterion σ(I): 2.4 / Redundancy: 3.7 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 2.1→6.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.11.0refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W3X

2w3x


Resolution: 2.1→14.84 Å / Cor.coef. Fo:Fc: 0.9547 / Cor.coef. Fo:Fc free: 0.9432 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.146 / Details: IDEAL-DISTANCE CONTACT TERM SETUP.
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2008 5.05 %RANDOM
Rwork0.161 ---
obs0.1627 39774 96.88 %-
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.1493 Å20 Å21.1108 Å2
2--0.9944 Å20 Å2
3---0.1549 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 16 546 5009
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014614HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1529SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes738HARMONIC5
X-RAY DIFFRACTIONt_it4614HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.79
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion554SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5387SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2533 169 5.83 %
Rwork0.1936 2731 -
all0.197 2900 -
obs--96.88 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodOrigin x (Å)Origin y (Å)Origin z (Å)L11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)
1refined-7.775911.69823.8792
2refined19.7641-3.895225.63211.0323-0.4402-0.16262.3269-0.14352.10310.02180.03170.1645-0.0083-0.0083-0.0434-0.3311-0.0572-0.0135-0.07160.01750.0226-0.05260.019-0.0451
3refined-2.7036-3.32639.53641.90290.71850.22920.56330.17871.1845-0.0083-0.1024-0.10760.0129-0.0229-0.05320.05010.11730.0312-0.0770.02620.0213-0.02730.0123-0.0041
41.1377-0.0419-0.39621.6051-0.48891.4290.0146-0.1445-0.10350.1126-0.02770.02870.09650.00170.0131-0.05050.01280.0202-0.0260.0144-0.0626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B)
2X-RAY DIFFRACTION2(CHAIN C)
3X-RAY DIFFRACTION3(CHAIN D)

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