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

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Basic information

Entry
Database: PDB / ID: 2xfl
TitleInduced-fit and allosteric effects upon polyene binding revealed by crystal structures of the Dynemicin thioesterase
ComponentsDYNE7
KeywordsHYDROLASE / POLYKETIDE BIOSYNTHESIS / ENEDIYNE / HOT-DOG FOLD
Function / homologyThioesterase-like superfamily / thiolester hydrolase activity / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / DynE7
Function and homology information
Biological speciesMICROMONOSPORA CHERSINA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiew, C.W. / Sharff, A. / Kotaka, M. / Kong, R. / Sun, H. / Bricogne, G. / Liang, Z. / 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. / 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 26, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
E: DYNE7
F: DYNE7
G: DYNE7
H: DYNE7


Theoretical massNumber of molelcules
Total (without water)127,0408
Polymers127,0408
Non-polymers00
Water2,882160
1
A: DYNE7
B: DYNE7
C: DYNE7
D: DYNE7


Theoretical massNumber of molelcules
Total (without water)63,5204
Polymers63,5204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-57.9 kcal/mol
Surface area23840 Å2
MethodPISA
2
E: DYNE7
F: DYNE7
G: DYNE7
H: DYNE7


Theoretical massNumber of molelcules
Total (without water)63,5204
Polymers63,5204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-56.2 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 179.127, 64.177
Angle α, β, γ (deg.)90.00, 111.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DYNE7


Mass: 15880.040 Da / Num. of mol.: 8 / Fragment: RESIDUES 3-144
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.37 Å3/Da / Density % sol: 48 % / 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 QUANTUM 315 / 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: 2.9→40 Å / Num. obs: 27578 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 66.02 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.7
Reflection shellResolution: 2.9→9.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 98

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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: 2.9→24.28 Å / Cor.coef. Fo:Fc: 0.8857 / Cor.coef. Fo:Fc free: 0.8476 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.392
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 1367 4.96 %RANDOM
Rwork0.1963 ---
obs0.1988 27544 98.56 %-
Displacement parametersBiso mean: 58.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.7414 Å20 Å2-13.7331 Å2
2---6.1327 Å20 Å2
3---8.874 Å2
Refine analyzeLuzzati coordinate error obs: 0.394 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8717 0 0 160 8877
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018947HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9712163HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2971SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1429HARMONIC5
X-RAY DIFFRACTIONt_it8947HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.19
X-RAY DIFFRACTIONt_other_torsion19.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1079SEMIHARMONIC5
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_contact9238SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.01 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2806 122 4.22 %
Rwork0.2027 2771 -
all0.2061 2893 -
obs--98.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)Origin x (Å)Origin y (Å)Origin z (Å)
13.98481.49430.21924.0433-1.00223.6204-0.14770.31790.0972-0.3308-0.02490.0614-0.28820.11650.1725-0.14860.0112-0.1558-0.2162-0.0097-0.029117.6609-6.2043-4.2658
23.13430.0071.32773.54690.52333.3024-0.0413-0.26850.0909-0.14410.06830.4415-0.1297-0.3674-0.027-0.22030.0148-0.1882-0.1868-0.01480.07185.4673-29.3593-8.375
33.54051.08961.65974.39221.29874.42680.0925-0.2646-0.23220.4374-0.0515-0.22940.1356-0.3041-0.0409-0.169-0.1611-0.1823-0.18380.0928-0.080623.8213-15.769414.5238
42.2060.45530.98685.24340.45952.51570.1790.1704-0.08220.0804-0.0203-0.80670.16830.3277-0.1587-0.2838-0.0338-0.2167-0.20590.06180.231525.1802-37.3877-1.1212
51.7527-1.40592.08984.9888-1.22485.5474-0.08390.05660.08950.5256-0.0126-0.2714-0.37410.56130.0965-0.0721-0.1576-0.2849-0.26760.0443-0.06742.404116.035231.746
64.37160.78530.67243.4713-1.0352.81050.1330.2085-0.13630.027-0.01110.03920.2071-0.3321-0.1219-0.19220.0037-0.2152-0.21630.00540.0696-11.9126.413118.0953
72.3714-0.93540.4614.6807-0.47883.9197-0.0987-0.2321-0.12190.8570.0210.0775-0.1958-0.33360.07770.062-0.0693-0.1962-0.3273-0.0324-0.1023-11.051137.951625.2018
80.9441-0.59192.01995.0884-1.78383.59040.16040.196-0.1991-0.3154-0.089-0.12030.26960.4833-0.0714-0.13280.1047-0.2178-0.2275-0.1054-0.0037-8.88729.34634.3647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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