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- PDB-4xae: Structure of Feruloyl-CoA 6-hydroxylase (F6H) from Arabidopsis th... -

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Basic information

Entry
Database: PDB / ID: 4xae
TitleStructure of Feruloyl-CoA 6-hydroxylase (F6H) from Arabidopsis thaliana
ComponentsFeruloyl CoA ortho-hydroxylase 1
KeywordsOXIDOREDUCTASE / PROTEIN ENGINEERING / COUMARINS / 2-oxoglutarate dependent dioxygenase
Function / homology
Function and homology information


feruloyl-CoA 6-hydroxylase / hydrogen peroxide-mediated programmed cell death / response to iron ion starvation / coumarin biosynthetic process / phenylpropanoid biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Feruloyl CoA ortho-hydroxylase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.769 Å
AuthorsZhou, D. / Kandavelu, P. / Zhang, H. / Wang, B.C. / Rose, J. / Yan, Y.
CitationJournal: Sci Rep / Year: 2015
Title: Structural Insights into Substrate Specificity of Feruloyl-CoA 6'-Hydroxylase from Arabidopsis thaliana.
Authors: Sun, X. / Zhou, D. / Kandavelu, P. / Zhang, H. / Yuan, Q. / Wang, B.C. / Rose, J. / Yan, Y.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Feruloyl CoA ortho-hydroxylase 1
B: Feruloyl CoA ortho-hydroxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6604
Polymers84,6142
Non-polymers462
Water50428
1
A: Feruloyl CoA ortho-hydroxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3302
Polymers42,3071
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Feruloyl CoA ortho-hydroxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3302
Polymers42,3071
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.219, 54.554, 78.815
Angle α, β, γ (deg.)90.00, 111.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Feruloyl CoA ortho-hydroxylase 1


Mass: 42306.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F6'H1, At3g13610, K20M4.5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LHN8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Sitting drop vapor diffusion at 291K using 2 microliter drops containing equal volumes of protein concentrate and a precipitant cocktail containing 20% (w/v) PEG-8000, 0.1 M MES, 0.3 M Ca(OAc)2, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2014
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→44.93 Å / Num. all: 19697 / Num. obs: 19697 / % possible obs: 92.21 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.795 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.01 / % possible all: 59.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GP4

1gp4


Resolution: 2.769→44.93 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2999 1869 9.99 %
Rwork0.2428 --
obs0.2484 18707 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.769→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5141 0 2 28 5171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065255
X-RAY DIFFRACTIONf_angle_d1.1947138
X-RAY DIFFRACTIONf_dihedral_angle_d14.4641936
X-RAY DIFFRACTIONf_chiral_restr0.05802
X-RAY DIFFRACTIONf_plane_restr0.007927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.769-2.84350.4283960.3245872X-RAY DIFFRACTION64
2.8435-2.92710.3811270.32871100X-RAY DIFFRACTION81
2.9271-3.02160.37731290.31771215X-RAY DIFFRACTION89
3.0216-3.12960.29821460.28861309X-RAY DIFFRACTION96
3.1296-3.25480.34951390.27641333X-RAY DIFFRACTION99
3.2548-3.40290.33361540.28041374X-RAY DIFFRACTION100
3.4029-3.58230.30681520.26831366X-RAY DIFFRACTION100
3.5823-3.80660.27451490.24271332X-RAY DIFFRACTION100
3.8066-4.10030.30581490.23841375X-RAY DIFFRACTION100
4.1003-4.51260.24881550.20891381X-RAY DIFFRACTION100
4.5126-5.16480.25891560.19431359X-RAY DIFFRACTION100
5.1648-6.50390.2781570.2431384X-RAY DIFFRACTION100
6.5039-44.93590.31831600.21651438X-RAY DIFFRACTION100
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)
11.1199-0.6666-0.71530.44270.2580.96940.09010.4032-0.277-0.0251-0.00550.12650.0332-0.06770.00010.3950.0642-0.04870.42430.01320.431661.621214.9831-22.4278
20.79890.0136-0.0671.014-0.06490.54620.02240.2472-0.0234-0.17380.0280.02360.0141-0.1608-0.00010.31670.02820.00160.32860.01650.383656.174719.1966-14.2415
30.568-0.0964-0.26440.37050.53750.7769-0.0342-0.00620.04760.04620.0797-0.07170.15270.29070.00020.36950.0091-0.01570.39620.05040.282389.4313-1.509120.1032
41.3968-0.826-0.32670.54360.38290.8557-0.03980.19530.0856-0.0659-0.00840.05670.06520.0358-0.00010.3174-0.031-0.00760.30590.03930.247380.87682.87216.4642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 343 )
3X-RAY DIFFRACTION3chain 'B' and (resid 15 through 136 )
4X-RAY DIFFRACTION4chain 'B' and (resid 137 through 344 )

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