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- PDB-6dd2: Crystal structure of Selaginella moellendorffii HCT -

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Basic information

Entry
Database: PDB / ID: 6dd2
TitleCrystal structure of Selaginella moellendorffii HCT
ComponentsProbable hydroxycinnamoyl transferase
KeywordsTRANSFERASE / BAHD acyltransferase
Function / homology
Function and homology information


shikimate O-hydroxycinnamoyltransferase / shikimate O-hydroxycinnamoyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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
Probable hydroxycinnamoyl transferase
Similarity search - Component
Biological speciesSelaginella moellendorffii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9056 Å
AuthorsLevsh, O. / Chiang, Y.C. / Lam, C.K. / Wang, Y. / Weng, J.K.
Funding support United States, 4items
OrganizationGrant numberCountry
Other privatePew Scholar Program in the Biomedical Sciences United States
Other privateSearle Scholars Program United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: PLoS Comput. Biol. / Year: 2018
Title: Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).
Authors: Chiang, Y.C. / Levsh, O. / Lam, C.K. / Weng, J.K. / Wang, Y.
History
DepositionMay 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Probable hydroxycinnamoyl transferase
B: Probable hydroxycinnamoyl transferase


Theoretical massNumber of molelcules
Total (without water)98,9892
Polymers98,9892
Non-polymers00
Water0
1
A: Probable hydroxycinnamoyl transferase


Theoretical massNumber of molelcules
Total (without water)49,4941
Polymers49,4941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable hydroxycinnamoyl transferase


Theoretical massNumber of molelcules
Total (without water)49,4941
Polymers49,4941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.390, 83.749, 188.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable hydroxycinnamoyl transferase


Mass: 49494.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: BAHDe7-1, SELMODRAFT_450171 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D8T7G0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, shikimate O-hydroxycinnamoyltransferase

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10.2 mg/mL SmHCT was used in a 2 uL protein, 1 uL reservoir solution hanging drop setup. The reservoir solution consisted of 0.1 M HEPES:NaOH, 2 M ammonium sulfate at pH 6.5.

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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: 2.81→61.54 Å / Num. obs: 15752 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 9
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2270 / Rpim(I) all: 0.345 / Rrim(I) all: 0.715 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KJS

5kjs


Resolution: 2.9056→42.502 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3066 2005 8.3 %
Rwork0.2486 --
obs0.2537 24166 84.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9056→42.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 0 0 6474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056644
X-RAY DIFFRACTIONf_angle_d0.7639039
X-RAY DIFFRACTIONf_dihedral_angle_d18.022445
X-RAY DIFFRACTIONf_chiral_restr0.047993
X-RAY DIFFRACTIONf_plane_restr0.0051176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9056-2.97820.3791070.32811280X-RAY DIFFRACTION69
2.9782-3.05870.38181310.31751346X-RAY DIFFRACTION74
3.0587-3.14870.33511270.30751426X-RAY DIFFRACTION77
3.1487-3.25030.38161370.29841439X-RAY DIFFRACTION79
3.2503-3.36640.3451240.28881449X-RAY DIFFRACTION79
3.3664-3.50120.35211350.2791475X-RAY DIFFRACTION79
3.5012-3.66040.34041350.26561466X-RAY DIFFRACTION80
3.6604-3.85330.34081550.26341683X-RAY DIFFRACTION91
3.8533-4.09450.29611490.23871603X-RAY DIFFRACTION87
4.0945-4.41040.2511590.21511736X-RAY DIFFRACTION92
4.4104-4.85360.27891560.19431737X-RAY DIFFRACTION93
4.8536-5.55460.27841590.21561788X-RAY DIFFRACTION95
5.5546-6.99320.26471600.251802X-RAY DIFFRACTION94
6.9932-42.50680.29451710.23651931X-RAY DIFFRACTION96

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