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- PDB-4g0b: Structure of native HCT from Coffea canephora -

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Basic information

Entry
Database: PDB / ID: 4g0b
TitleStructure of native HCT from Coffea canephora
ComponentsHydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
KeywordsTRANSFERASE / BAHD Superfamily / hydroxycinnamoyl transferase
Function / homologyTransferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / 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: 3 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 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
B: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9647
Polymers96,4842
Non-polymers4805
Water50428
1
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5304
Polymers48,2421
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,2421
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules

A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0608
Polymers96,4842
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1820 Å2
ΔGint-80 kcal/mol
Surface area35090 Å2
MethodPISA
4
B: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules

B: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8686
Polymers96,4842
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3300 Å2
ΔGint-61 kcal/mol
Surface area33990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.100, 116.100, 158.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 1 - 434 / Label seq-ID: 3 - 436

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase


Mass: 48241.852 Da / Num. of mol.: 2
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, shikimate O-hydroxycinnamoyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M magnesium sulfate and 0.1 M MES, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 5, 2008 / Details: KB-mirror system
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 72116 / Num. obs: 22073 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.166 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3.1 / Num. unique all: 10301 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BGH

2bgh


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.879 / SU B: 38.688 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25004 1133 5.1 %RANDOM
Rwork0.18599 ---
obs0.1893 21010 98.73 %-
all-22073 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6547 0 25 28 6600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026745
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9679178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30623.085295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.381151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4751547
X-RAY DIFFRACTIONr_chiral_restr0.0970.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215205
Refine LS restraints NCS

Ens-ID: 1 / Number: 465 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.22 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 81 -
Rwork0.27 1361 -
obs--99.17 %
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)
11.1503-0.2478-0.2541.3182-0.09061.1405-0.02680.1376-0.2086-0.18640.0636-0.01890.1413-0.0353-0.03680.1104-0.0034-0.01430.026-0.03390.0541-40.897-21.13922.047
21.31560.09420.31240.975-0.13840.8347-0.0275-0.09720.07010.05840.0526-0.0324-0.13380.0215-0.02510.12420.01280.01360.0173-0.00950.0093-25.37-27.22461.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 434
2X-RAY DIFFRACTION2B1 - 434

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