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- PDB-4g2m: Structure of a Lys-HCT mutant from Coffea canephora (Crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 4g2m
TitleStructure of a Lys-HCT mutant from Coffea canephora (Crystal form 2)
ComponentsHydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
KeywordsTRANSFERASE / BAHD Superfamily / hydroxycinnamoyl transferase
Function / homology: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
Function and homology information
Biological speciesCoffea canephora (robusta coffee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLallemand, L.A. / McCarthy, J.G. / McCarthy, A.A.
CitationJournal: Plant Physiol. / Year: 2012
Title: A structural basis for the biosynthesis of the major chlorogenic acids found in coffee.
Authors: Lallemand, L.A. / Zubieta, C. / Lee, S.G. / Wang, Y. / Acajjaoui, S. / Timmins, J. / McSweeney, S. / Jez, J.M. / McCarthy, J.G. / McCarthy, A.A.
History
DepositionJul 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase


Theoretical massNumber of molelcules
Total (without water)48,4171
Polymers48,4171
Non-polymers00
Water48627
1
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase

A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase


Theoretical massNumber of molelcules
Total (without water)96,8342
Polymers96,8342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2270 Å2
ΔGint-11 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.550, 96.280, 118.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase


Mass: 48416.977 Da / Num. of mol.: 1 / Mutation: K210A, K217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coffea canephora (robusta coffee) / Gene: HCT / Plasmid: pProEX_HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS / References: UniProt: A4ZKE4, EC: 2.3.1.99
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 45.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 15% PEG 4000, 0.2 M MgCl2 and 0.1 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2009 / Details: Toroidal mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 59400 / Num. obs: 15066 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.64
Reflection shellResolution: 2.5→2.5 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.88 / Num. unique all: 6492 / % possible all: 94.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 26.607 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.67 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25407 775 5 %RANDOM
Rwork0.19388 ---
obs0.19699 14696 99.47 %-
all-15066 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.652 Å2
Baniso -1Baniso -2Baniso -3
1-6.4 Å20 Å20 Å2
2---3.03 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 0 27 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023297
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9644498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14623.5140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80815491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4481519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212561
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 49 -
Rwork0.27 1002 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: -17.7045 Å / Origin y: -22.5635 Å / Origin z: 11.5391 Å
111213212223313233
T0.0453 Å2-0.0368 Å2-0.0369 Å2-0.0497 Å20.0289 Å2--0.0415 Å2
L0.2974 °2-0.196 °20.566 °2-1.3886 °2-0.6578 °2--1.3554 °2
S0.007 Å °-0.0755 Å °-0.0262 Å °-0.0779 Å °0.0605 Å °0.1406 Å °0.01 Å °-0.1235 Å °-0.0675 Å °

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