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- PDB-5kjv: Crystal structure of Coleus blumei HCT -

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Basic information

Entry
Database: PDB / ID: 5kjv
TitleCrystal structure of Coleus blumei HCT
ComponentsHydroxycinnamoyl transferase
KeywordsTRANSFERASE / phenylpropanoid metabolism / BAHD / HCT / acyltransferase
Function / homologyshikimate O-hydroxycinnamoyltransferase / shikimate O-hydroxycinnamoyltransferase activity / Transferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Hydroxycinnamoyl transferase
Function and homology information
Biological speciesPlectranthus scutellarioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsLevsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
Searle Scholars Program United States
Pew Scholars Program in the Biomedical Sciences United States
Howard Hughes Medical Institute (HHMI) 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
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxycinnamoyl transferase
B: Hydroxycinnamoyl transferase


Theoretical massNumber of molelcules
Total (without water)94,3552
Polymers94,3552
Non-polymers00
Water19,1681064
1
A: Hydroxycinnamoyl transferase


Theoretical massNumber of molelcules
Total (without water)47,1781
Polymers47,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydroxycinnamoyl transferase


Theoretical massNumber of molelcules
Total (without water)47,1781
Polymers47,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.550, 56.690, 107.840
Angle α, β, γ (deg.)83.22, 89.65, 72.29
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.) Plectranthus scutellarioides (plant) / Gene: cbhct2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E8ZAP2, shikimate O-hydroxycinnamoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1064 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
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

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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: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→53.6 Å / Num. obs: 199588 / % possible obs: 90.2 % / Redundancy: 2.6 % / Net I/σ(I): 5.8

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 1.75→50.454 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 23.78
RfactorNum. reflection% reflection
Rfree0.2112 4002 2.62 %
Rwork0.1705 --
obs0.1716 152836 90.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→50.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 0 1064 7714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0196832
X-RAY DIFFRACTIONf_angle_d1.4599306
X-RAY DIFFRACTIONf_dihedral_angle_d13.2442484
X-RAY DIFFRACTIONf_chiral_restr0.0521024
X-RAY DIFFRACTIONf_plane_restr0.0081212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77060.3782460.25991972X-RAY DIFFRACTION34
1.7706-1.79220.269760.28522174X-RAY DIFFRACTION38
1.7922-1.81490.34271040.26743898X-RAY DIFFRACTION70
1.8149-1.83880.32851260.26784997X-RAY DIFFRACTION88
1.8388-1.8640.28271440.25915130X-RAY DIFFRACTION89
1.864-1.89060.3311280.26895205X-RAY DIFFRACTION91
1.8906-1.91880.33861330.27285188X-RAY DIFFRACTION93
1.9188-1.94880.25611440.24965297X-RAY DIFFRACTION93
1.9488-1.98080.25681400.23265388X-RAY DIFFRACTION92
1.9808-2.01490.27431580.22055320X-RAY DIFFRACTION96
2.0149-2.05160.25211540.21775379X-RAY DIFFRACTION95
2.0516-2.0910.2861410.21145413X-RAY DIFFRACTION93
2.091-2.13370.23231480.18445466X-RAY DIFFRACTION97
2.1337-2.18010.24371400.18095482X-RAY DIFFRACTION96
2.1801-2.23080.2321540.18085443X-RAY DIFFRACTION95
2.2308-2.28660.24411560.18735375X-RAY DIFFRACTION96
2.2866-2.34840.21371400.16225530X-RAY DIFFRACTION95
2.3484-2.41750.2231420.16535454X-RAY DIFFRACTION97
2.4175-2.49560.19481440.15955558X-RAY DIFFRACTION96
2.4956-2.58480.21681500.16135380X-RAY DIFFRACTION96
2.5848-2.68820.20931560.16585490X-RAY DIFFRACTION95
2.6882-2.81060.21761360.16935468X-RAY DIFFRACTION97
2.8106-2.95870.2161380.17535534X-RAY DIFFRACTION97
2.9587-3.14410.2131480.16715580X-RAY DIFFRACTION97
3.1441-3.38680.21421460.1565524X-RAY DIFFRACTION97
3.3868-3.72750.16761560.13735500X-RAY DIFFRACTION97
3.7275-4.26670.14911460.12625543X-RAY DIFFRACTION98
4.2667-5.37460.15491520.11375606X-RAY DIFFRACTION98
5.3746-50.47470.15371560.14535540X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -42.0732 Å / Origin y: 17.8632 Å / Origin z: -4.114 Å
111213212223313233
T0.0318 Å2-0.0052 Å2-0.0061 Å2-0.0756 Å2-0.0002 Å2--0.0802 Å2
L-0.0142 °2-0.0074 °2-0.1038 °2-0.0834 °20.0554 °2--0.6488 °2
S0.0209 Å °0.0119 Å °0.0069 Å °0.0049 Å °0.0071 Å °-0.0032 Å °0.0039 Å °-0.0311 Å °0.0026 Å °
Refinement TLS groupSelection details: all

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