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- PDB-5kjw: Crystal structure of Coleus blumei HCT in complex with 3-hydroxya... -

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Basic information

Entry
Database: PDB / ID: 5kjw
TitleCrystal structure of Coleus blumei HCT in complex with 3-hydroxyacetophenone
ComponentsHydroxycinnamoyl transferase
KeywordsTRANSFERASE / phenylpropanoid metabolism / BAHD / HCT / acyltransferase
Function / homology
Function and homology information


shikimate O-hydroxycinnamoyltransferase / shikimate O-hydroxycinnamoyltransferase activity
Similarity search - Function
Transferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-(3-hydroxyphenyl)ethanone / Hydroxycinnamoyl transferase
Similarity search - Component
Biological speciesSolenostemon scutellarioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLevsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Searle Scholars Program United States
Pew Scholars Program in the Biomedical Sciences United States
CitationJournal: Biochemistry / Year: 2016
Title: Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase.
Authors: Levsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxycinnamoyl transferase
B: Hydroxycinnamoyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6284
Polymers94,3552
Non-polymers2722
Water15,583865
1
A: Hydroxycinnamoyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3142
Polymers47,1781
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydroxycinnamoyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3142
Polymers47,1781
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.080, 56.390, 107.950
Angle α, β, γ (deg.)96.96, 90.00, 107.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hydroxycinnamoyl transferase


Mass: 47177.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solenostemon scutellarioides (plant) / Gene: cbhct2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E8ZAP2, shikimate O-hydroxycinnamoyltransferase
#2: Chemical ChemComp-53C / 1-(3-hydroxyphenyl)ethanone / 3-Hydroxyacetophenone


Mass: 136.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-Tris:HCl, 25% PEG 3350, pH 7.5. A soaking drop was prepared with 10% (v/v) of 500 mM 3-hydroxyacetophenone, and 10% (v/v) of 100 mM p-coumaroyl CoA, in reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→53.54 Å / Num. obs: 95145 / % possible obs: 87.7 % / Redundancy: 2.7 % / Net I/σ(I): 5.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 1.9→53.537 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 3466 3.64 %
Rwork0.218 --
obs0.2197 95142 73.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→53.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 20 865 7463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036814
X-RAY DIFFRACTIONf_angle_d0.7229280
X-RAY DIFFRACTIONf_dihedral_angle_d10.9242476
X-RAY DIFFRACTIONf_chiral_restr0.0311014
X-RAY DIFFRACTIONf_plane_restr0.0051210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9260.3618940.33442104X-RAY DIFFRACTION42
1.926-1.95360.3461760.31722239X-RAY DIFFRACTION44
1.9536-1.98270.3489830.31572296X-RAY DIFFRACTION47
1.9827-2.01370.33151050.30432499X-RAY DIFFRACTION49
2.0137-2.04670.294830.28672570X-RAY DIFFRACTION51
2.0467-2.0820.362980.2892489X-RAY DIFFRACTION50
2.082-2.11990.3132900.28112500X-RAY DIFFRACTION50
2.1199-2.16060.3258970.27172500X-RAY DIFFRACTION50
2.1606-2.20470.3012850.26882504X-RAY DIFFRACTION49
2.2047-2.25270.3165830.25532475X-RAY DIFFRACTION49
2.2527-2.30510.3115880.26212711X-RAY DIFFRACTION53
2.3051-2.36270.28831740.25274288X-RAY DIFFRACTION87
2.3627-2.42660.2881460.26214362X-RAY DIFFRACTION87
2.4266-2.4980.31981700.24464347X-RAY DIFFRACTION86
2.498-2.57860.28971900.24454546X-RAY DIFFRACTION90
2.5786-2.67080.29921740.25184565X-RAY DIFFRACTION91
2.6708-2.77770.28081770.23344536X-RAY DIFFRACTION91
2.7777-2.90420.29861830.23124737X-RAY DIFFRACTION94
2.9042-3.05730.2681820.22034756X-RAY DIFFRACTION95
3.0573-3.24880.27511700.1944677X-RAY DIFFRACTION94
3.2488-3.49960.22531900.18324778X-RAY DIFFRACTION95
3.4996-3.85170.18911770.16264783X-RAY DIFFRACTION94
3.8517-4.40880.20591820.15724739X-RAY DIFFRACTION94
4.4088-5.55370.21081840.16664768X-RAY DIFFRACTION95
5.5537-53.5580.22451850.18654907X-RAY DIFFRACTION98

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