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- PDB-3w05: Crystal structure of Oryza sativa DWARF14 (D14) in complex with PMSF -

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Basic information

Entry
Database: PDB / ID: 3w05
TitleCrystal structure of Oryza sativa DWARF14 (D14) in complex with PMSF
ComponentsDwarf 88 esterase
KeywordsSIGNALING PROTEIN / STRIGOLACTONE SIGNALING / ALPHA/BETA HYDROLASE / STRIGOLACTONE Hydrolysis
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 1.58 Å
AuthorsKagiyama, M. / Hirano, Y. / Mori, T. / Kim, S.Y. / Kyozuka, J. / Seto, Y. / Yamaguchi, S. / Hakoshima, T.
CitationJournal: Genes Cells / Year: 2013
Title: Structures of D14 and D14L in the strigolactone and karrikin signaling pathways
Authors: Kagiyama, M. / Hirano, Y. / Mori, T. / Kim, S.Y. / Kyozuka, J. / Seto, Y. / Yamaguchi, S. / Hakoshima, T.
History
DepositionOct 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 8, 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_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dwarf 88 esterase
B: Dwarf 88 esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,16211
Polymers58,3832
Non-polymers7799
Water7,764431
1
A: Dwarf 88 esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6126
Polymers29,1921
Non-polymers4205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dwarf 88 esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5505
Polymers29,1921
Non-polymers3584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.300, 88.518, 118.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dwarf 88 esterase / Hydrolase / alpha/beta fold family protein / expressed / Os03g0203200 protein


Mass: 29191.555 Da / Num. of mol.: 2 / Fragment: UNP residues 55-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: D88, LOC_Os03g10620, Os03g0203200 / Plasmid: PET47B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q10QA5
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG6000, 5% MPD, 0.1M Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Details: mirrors
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 70618 / Num. obs: 69842 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.095
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 3 % / Num. unique all: 6484 / Rsym value: 0.493 / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLREP
Starting model: 1WOM

1wom


Resolution: 1.58→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.096 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19434 3501 5 %RANDOM
Rwork0.16622 ---
obs0.16763 66026 98.46 %-
all-70614 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.39 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.58→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 48 431 4565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9655994
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.25522.083192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12615688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7771544
X-RAY DIFFRACTIONr_chiral_restr0.1110.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213378
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7891.52737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.78724445
X-RAY DIFFRACTIONr_scbond_it4.33431648
X-RAY DIFFRACTIONr_scangle_it6.4524.51534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 253 -
Rwork0.232 4445 -
obs-4698 91.51 %
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)
10.440.1027-0.08870.425-0.0170.478-0.0541-0.04110.0312-0.01110.0404-0.00110.01190.01040.01360.00780.0098-0.00330.029-0.00560.0242-18.525914.8312-18.4063
20.2883-0.07820.06540.6649-0.16790.51550.02960.02970-0.0998-0.02610.00250.09490.0042-0.00350.03580.0086-0.00480.0101-0.00460.0034-33.1848-8.92948.5619
30.07440.0946-0.04830.1859-0.17410.4014-0.00790.00970.0019-0.02910.0177-0.00560.05810.0076-0.00980.02720.01460.00220.0165-0.00430.0189-24.81083.623-7.2421
40.79120.0490.00610.12990.12210.1169-0.0010.01890.02160.05010.0294-0.01220.04580.0415-0.02830.06190.03430.00540.0817-0.04560.0396-27.1910.7032-4.6171
50.09260.1661-0.15230.6239-0.51170.49230.0542-0.00260.02810.00090.0470.1470.04160.0099-0.10120.10770.0189-0.00480.05540.00890.0527-27.97552.2993-7.3628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 318
2X-RAY DIFFRACTION2B55 - 318
3X-RAY DIFFRACTION3A501 - 728
4X-RAY DIFFRACTION3B501 - 703
5X-RAY DIFFRACTION4A401
6X-RAY DIFFRACTION4B401
7X-RAY DIFFRACTION5A402 - 405
8X-RAY DIFFRACTION5B402 - 404

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