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- PDB-5vg2: Intradiol ring-cleavage Dioxygenase from Tetranychus urticae -

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Basic information

Entry
Database: PDB / ID: 5vg2
TitleIntradiol ring-cleavage Dioxygenase from Tetranychus urticae
ComponentsIntradiol ring-cleavage Dioxygenase
KeywordsOXIDOREDUCTASE / Tetranychus urticae / Dioxygenase / Catechol / intradiol ring-cleavage
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 / CACODYLATE ION / : / 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: 2.46 Å
AuthorsSchlachter, C. / Klapper, V. / 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
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 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 1.2Oct 4, 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_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.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
Revision 1.3Oct 23, 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
U: Intradiol ring-cleavage Dioxygenase
A: Intradiol ring-cleavage Dioxygenase
B: Intradiol ring-cleavage Dioxygenase
C: Intradiol ring-cleavage Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,71017
Polymers105,2544
Non-polymers1,45613
Water2,522140
1
U: Intradiol ring-cleavage Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5063
Polymers26,3141
Non-polymers1932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Intradiol ring-cleavage Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5063
Polymers26,3141
Non-polymers1932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Intradiol ring-cleavage Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6434
Polymers26,3141
Non-polymers3303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Intradiol ring-cleavage Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0547
Polymers26,3141
Non-polymers7416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.494, 43.067, 165.708
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11U
21A
12U
22B
13U
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: _ / 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: 9 - 212

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11UA
21AB
12UA
22BC
13UA
23CD
14AB
24BC
15AB
25CD
16BC
26CD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Intradiol ring-cleavage Dioxygenase


Mass: 26313.551 Da / Num. of mol.: 4 / Fragment: UNP residues 48-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Production host: Escherichia coli (E. coli) / References: UniProt: T1K8P1
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.5, 15% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 30081 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.064 / Rrim(I) all: 0.116 / Rsym value: 0.077 / Net I/σ(I): 14.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / Num. unique obs: 1539 / Rpim(I) all: 0.371 / Rrim(I) all: 0.665 / Rsym value: 0.483 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ILT

4ilt


Resolution: 2.46→50.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.871 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23097 1414 4.7 %RANDOM
Rwork0.19123 ---
obs0.19314 28666 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.706 Å2
Baniso -1Baniso -2Baniso -3
1--7.21 Å20 Å20.73 Å2
2--5.35 Å20 Å2
3---1.7 Å2
Refinement stepCycle: 1 / Resolution: 2.46→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6460 0 49 140 6649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196666
X-RAY DIFFRACTIONr_bond_other_d00.025957
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9489047
X-RAY DIFFRACTIONr_angle_other_deg3.727313825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46523.818330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.878151077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5561546
X-RAY DIFFRACTIONr_chiral_restr0.0960.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217412
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021386
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_it1.8452.8423242
X-RAY DIFFRACTIONr_mcbond_other1.8442.8413241
X-RAY DIFFRACTIONr_mcangle_it3.1424.2494042
X-RAY DIFFRACTIONr_mcangle_other3.1424.2494043
X-RAY DIFFRACTIONr_scbond_it2.2553.0813424
X-RAY DIFFRACTIONr_scbond_other2.2553.0843425
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3814.5455006
X-RAY DIFFRACTIONr_long_range_B_refined6.86532.2067074
X-RAY DIFFRACTIONr_long_range_B_other6.88332.1867070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11U131160.07
12A131160.07
21U127260.09
22B127260.09
31U127960.09
32C127960.09
41A127000.09
42B127000.09
51A129500.09
52C129500.09
61B129140.07
62C129140.07
LS refinement shellResolution: 2.457→2.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 103 -
Rwork0.271 2007 -
obs--90.17 %
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)
12.05660.21110.20110.5853-0.73783.0149-0.0049-0.06690.04890.04450.01490.00250.13250.0053-0.00990.54120.02610.00490.0572-0.00510.09333.318-2.07461.592
223.35590.4141.23223.30341.99745.4067-0.28510.84631.0205-0.12250.1759-0.0552-0.18770.48040.10910.44080.01520.03680.08850.05230.248538.14615.19252.505
31.98980.0205-0.48960.67070.43261.98890.0115-0.032-0.09110.01120.0369-0.03090.18690.0909-0.04830.570.0111-0.01750.05340.0090.058936.702-4.54454.834
43.45071.1881.19682.66961.08953.10850.1163-0.1484-0.2430.1537-0.076-0.03780.38140.243-0.04040.58560.0447-0.01720.08570.00070.107540.473-8.26161.999
52.9885-0.5722-0.97250.74790.09511.5695-0.0225-0.20510.13680.04030.0018-0.1145-0.0222-0.05250.02060.51740.0255-0.03340.1090.00770.05549.6458.69365.232
61.3543-0.6344-1.37721.30690.51773.13790.0238-0.0673-0.0643-0.0503-0.017-0.06910.126-0.1698-0.00690.4734-0.0013-0.0030.13680.02840.09610.8912.13158.472
74.335-0.7976-0.02871.2329-0.02090.00510.08090.39610.3251-0.0509-0.0826-0.0704-0.0062-0.02580.00170.51650.02690.00280.17380.03160.08031.92112.35856.312
83.8732-0.7904-0.84331.4419-0.22022.76-0.046-0.40630.63760.07040.0767-0.0074-0.1556-0.3392-0.03070.5243-0.0016-0.03490.1444-0.06120.16361.63712.6667.082
92.11541.1841-1.01551.4227-1.09412.79840.08280.0662-0.03590.0767-0.0959-0.0155-0.1510.14570.0130.5328-0.00990.00360.12260.01030.006744.87311.50121.697
1034.7788-2.52730.20322.39453.61016.0259-0.2414-1.3611.66480.44360.1742-0.13880.69610.41890.06730.6632-0.24460.02631.30980.23280.191252.0815.03839.111
118.0732-6.75980.18826.50890.15812.64120.30650.0571-0.0444-0.1425-0.13420.221-0.25830.562-0.17220.5377-0.12870.03310.1842-0.02930.196756.42520.54523.658
124.9413-0.6551-3.40752.4283-0.51659.98170.49350.6030.1063-0.268-0.7674-0.0488-0.6736-0.24320.27390.4215-0.00840.00530.3350.00010.076647.92615.85715.83
132.63850.22490.15380.8808-0.15372.1648-0.07480.30560.00940.00240.1407-0.02610.1049-0.1746-0.06590.4786-0.04120.01660.2062-0.00690.004819.7111.99219.963
1435.8696-2.900410.97530.3783-0.410210.3327-0.7732-1.60852.04110.2657-0.0477-0.1934-0.8986-0.84770.82090.796-0.1547-0.05890.39110.03690.228913.77317.24932.018
151.64590.1979-0.33420.8383-0.41852.4460.01020.2144-0.0859-0.03320.07290.02410.1571-0.2931-0.0830.4823-0.0088-0.0130.1771-0.00960.009917.91-1.06125.474
163.6493-1.0145-0.43222.1865-1.26982.4313-0.04650.2693-0.37620.02640.13640.17370.2346-0.4921-0.08980.4878-0.0811-0.07670.2061-0.00320.05710.711-3.73120.763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 122
2X-RAY DIFFRACTION2A123 - 137
3X-RAY DIFFRACTION3A138 - 217
4X-RAY DIFFRACTION4A218 - 259
5X-RAY DIFFRACTION5B56 - 116
6X-RAY DIFFRACTION6B117 - 156
7X-RAY DIFFRACTION7B157 - 217
8X-RAY DIFFRACTION8B218 - 259
9X-RAY DIFFRACTION9C56 - 200
10X-RAY DIFFRACTION10C201 - 210
11X-RAY DIFFRACTION11C211 - 233
12X-RAY DIFFRACTION12C234 - 259
13X-RAY DIFFRACTION13U56 - 122
14X-RAY DIFFRACTION14U123 - 136
15X-RAY DIFFRACTION15U137 - 208
16X-RAY DIFFRACTION16U209 - 259

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