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- PDB-6bdj: Crystal structure of dioxygenase Tetur07g02040 -

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Basic information

Entry
Database: PDB / ID: 6bdj
TitleCrystal structure of dioxygenase Tetur07g02040
ComponentsTetur07g02040
KeywordsMETAL BINDING PROTEIN / dioxygenase / two-spotted spider mite / agricultural pest / detoxification
Function / homologyIntradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferric iron binding / : / Intradiol ring-cleavage dioxygenases domain-containing protein
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDaneshian, L. / Schlachter, C.R. / Chruszcz, M.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2019
Title: Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch.
Authors: Schlachter, C.R. / Daneshian, L. / Amaya, J. / Klapper, V. / Wybouw, N. / Borowski, T. / Van Leeuwen, T. / Grbic, V. / Grbic, M. / Makris, T.M. / Chruszcz, M.
History
DepositionOct 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetur07g02040
U: Tetur07g02040
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9784
Polymers55,8672
Non-polymers1122
Water1,56787
1
A: Tetur07g02040
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9892
Polymers27,9331
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
U: Tetur07g02040
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9892
Polymers27,9331
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.091, 45.415, 83.040
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21U

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 56 - 259 / Label seq-ID: 34 - 237

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

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Components

#1: Protein Tetur07g02040


Mass: 27933.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107361576 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: T1K8P1
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M LiSO4, 0.1 M HEPES pH 7.5, 10%w/v PEG3350, 10 mM catechol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 24133 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.064 / Rsym value: 0.056 / Net I/σ(I): 32
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 929 / CC1/2: 0.963 / Rpim(I) all: 0.16 / Rrim(I) all: 0.3 / Rsym value: 0.252 / % possible all: 72.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.208 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24827 1095 4.6 %RANDOM
Rwork0.21429 ---
obs0.21592 22883 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.448 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å2-0 Å2-0.6 Å2
2--5.61 Å20 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 2 87 3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193263
X-RAY DIFFRACTIONr_bond_other_d00.022845
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.944441
X-RAY DIFFRACTIONr_angle_other_deg3.83836591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40123.765162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0415498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4911522
X-RAY DIFFRACTIONr_chiral_restr0.10.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213687
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02691
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_it1.8924.2351613
X-RAY DIFFRACTIONr_mcbond_other1.8934.2351612
X-RAY DIFFRACTIONr_mcangle_it3.1096.3372011
X-RAY DIFFRACTIONr_mcangle_other3.1096.3382012
X-RAY DIFFRACTIONr_scbond_it1.7714.2971650
X-RAY DIFFRACTIONr_scbond_other1.774.2981651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9226.4022431
X-RAY DIFFRACTIONr_long_range_B_refined5.62449.1033565
X-RAY DIFFRACTIONr_long_range_B_other5.61448.9683553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12418 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2U
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 62 -
Rwork0.266 1321 -
obs--76.2 %
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)
17.52881.8373-2.0021.4284-1.49032.20960.62280.14880.5110.3285-0.42770.0706-0.38630.4633-0.1950.1269-0.11040.07550.2641-0.00020.089547.79112.64521.447
24.72090.7513-1.89691.1615-1.22354.84450.09680.9078-0.06240.02040.26980.1924-0.0782-0.7975-0.36670.0107-0.00790.0180.3335-0.02560.084917.3030.53823.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 259
2X-RAY DIFFRACTION2U55 - 259

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