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- PDB-4g22: Structure of a Lys-HCT mutant from Coffea canephora (Crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 4g22
TitleStructure of a Lys-HCT mutant from Coffea canephora (Crystal form 1)
ComponentsHydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
KeywordsTRANSFERASE / BAHD Superfamily / hydroxycinnamoyltransferase
Function / homologyrosmarinate synthase activity / : / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 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: 1.7 Å
AuthorsMcCarthy, A.A. / Lallemand, L.A. / McCarthy, J.G.
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 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 27, 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 / struct_site
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 / _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)97,2137
Polymers96,8662
Non-polymers3475
Water11,259625
1
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6534
Polymers48,4331
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5613
Polymers48,4331
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules

B: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2137
Polymers96,8662
Non-polymers3475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area3230 Å2
ΔGint-35 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.550, 116.480, 118.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.990533, 0.088179, 0.105211), (-0.087602, -0.996104, 0.010103), (0.105692, 0.00079, 0.994399)-5.83493, 3.7352, -3.03072

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Components

#1: Protein Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase


Mass: 48432.977 Da / Num. of mol.: 2 / Mutation: K210A/K217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coffea canephora (robusta coffee) / Gene: HCT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS
References: UniProt: A4ZKE4, shikimate O-hydroxycinnamoyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
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: 0.984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2009 / Details: toroidal mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 96736 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.8 / % possible all: 83.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0116refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.059 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20271 952 1 %RANDOM
Rwork0.16751 ---
obs0.16784 96736 99.74 %-
all-96980 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.58 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6423 0 20 625 7068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.026712
X-RAY DIFFRACTIONr_angle_refined_deg2.3261.9699160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8523.096281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.007151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6961544
X-RAY DIFFRACTIONr_chiral_restr0.1920.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215185
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 64 -
Rwork0.264 6607 -
obs--99.39 %
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)
10.2296-0.2320.18190.554-0.28410.7342-0.0374-0.03740.01180.04740.0462-0.0163-0.0531-0.0468-0.00880.00780.00580.00320.020400.0364-14.3864-15.35026.7018
20.1885-0.2178-0.14020.61280.34391.0223-0.0333-0.0115-0.05060.05670.00820.08860.1051-0.04540.02510.0138-0.0070.00850.0261-0.0050.06111.226918.2938.547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 434
2X-RAY DIFFRACTION2B0 - 434

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