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- PDB-4k02: Crystal structure of AtDHNAT1, a 1,4-dihydroxy-2-naphthoyl-CoA th... -

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Basic information

Entry
Database: PDB / ID: 4k02
TitleCrystal structure of AtDHNAT1, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Arabidopsis thaliana
Components1,4-dihydroxy-2-naphthoyl-CoA thioesterase
KeywordsHYDROLASE / hotdog fold / thioesterase
Function / homology
Function and homology information


acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / peroxisome / protein homotetramerization
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
1,4-dihydroxy-2-naphthoyl-CoA thioesterase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFurt, F. / Allen, W.J. / Widhalm, J.R. / Madzelan, P. / Rizzo, R.C. / Basset, G. / Wilson, M.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis.
Authors: Furt, F. / Allen, W.J. / Widhalm, J.R. / Madzelan, P. / Rizzo, R.C. / Basset, G. / Wilson, M.A.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,4-dihydroxy-2-naphthoyl-CoA thioesterase
B: 1,4-dihydroxy-2-naphthoyl-CoA thioesterase


Theoretical massNumber of molelcules
Total (without water)34,0322
Polymers34,0322
Non-polymers00
Water93752
1
A: 1,4-dihydroxy-2-naphthoyl-CoA thioesterase
B: 1,4-dihydroxy-2-naphthoyl-CoA thioesterase

A: 1,4-dihydroxy-2-naphthoyl-CoA thioesterase
B: 1,4-dihydroxy-2-naphthoyl-CoA thioesterase


Theoretical massNumber of molelcules
Total (without water)68,0634
Polymers68,0634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+8/31
Buried area7440 Å2
ΔGint-36 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.529, 99.529, 61.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 10 - 136 / Label seq-ID: 13 - 139

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

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Components

#1: Protein 1,4-dihydroxy-2-naphthoyl-CoA thioesterase / F11A17.13 / Thioesterase-like protein


Mass: 17015.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g48320, F11A17.13 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SX65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.7 M NaHCOOH, 100 mM Tris-HCl, 10 mM n-octyl- D-glucoside in protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→28.88 Å / Num. all: 26984 / Num. obs: 26984 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 35.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 48.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.4 / % possible all: 84.1

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SC0

1sc0


Resolution: 1.9→28.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.182 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21055 1361 5.1 %RANDOM
Rwork0.18318 ---
all0.18451 26702 --
obs0.18451 26702 95.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.246 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-1.2 Å20 Å2
2---1.2 Å20 Å2
3---3.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 52 1966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191961
X-RAY DIFFRACTIONr_bond_other_d0.0010.021963
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9712659
X-RAY DIFFRACTIONr_angle_other_deg0.84234536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5835254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34424.06264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.782158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212154
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02406
Refine LS restraints NCS

Ens-ID: 1 / Number: 7558 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 91 -
Rwork0.304 1539 -
obs-1630 79.36 %
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)
15.8291.4483-1.07094.6254-0.82042.08040.27060.1701-0.4932-0.0714-0.0187-0.1690.1327-0.116-0.25190.13750.0604-0.02470.0516-0.00860.216142.1536-16.362681.1741
24.20780.02090.61275.4786-1.53093.71290.4417-0.761-0.00620.797-0.2036-0.1813-0.2011-0.0582-0.23810.3703-0.10580.11420.1993-0.01340.210939.6448-5.602396.9636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 136
2X-RAY DIFFRACTION2B10 - 136

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