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- PDB-5td3: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia v... -

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Basic information

Entry
Database: PDB / ID: 5td3
TitleCrystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis
ComponentsCatechol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / catechol 1 / 2-dioxygenase / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function
Catechol 1,2-dioxygenase, proteobacteria / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis
Authors: Conrady, D.G. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionSep 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 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 / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_symmetry / _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: Catechol 1,2-dioxygenase
B: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73711
Polymers68,9192
Non-polymers1,8189
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-163 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.410, 55.860, 85.690
Angle α, β, γ (deg.)90.000, 116.300, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11:26 or resid 29:30 or resid...
21(chain B and ((resid 11 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEALAALA(chain A and (resid 11:26 or resid 29:30 or resid...AA11 - 2611 - 26
12ALAALAASNASN(chain A and (resid 11:26 or resid 29:30 or resid...AA29 - 3029 - 30
13SERSERGLYGLY(chain A and (resid 11:26 or resid 29:30 or resid...AA35 - 7735 - 77
14ASPASPGLYGLY(chain A and (resid 11:26 or resid 29:30 or resid...AA79 - 13079 - 130
15ALAALAGLYGLY(chain A and (resid 11:26 or resid 29:30 or resid...AA132 - 149132 - 149
16VALVALVALVAL(chain A and (resid 11:26 or resid 29:30 or resid...AA151 - 193151 - 193
17THRTHRVALVAL(chain A and (resid 11:26 or resid 29:30 or resid...AA195 - 240195 - 240
18SERSERTHRTHR(chain A and (resid 11:26 or resid 29:30 or resid...AA242 - 250242 - 250
19PHEPHELYSLYS(chain A and (resid 11:26 or resid 29:30 or resid...AA252 - 279252 - 279
110THRTHRTHRTHR(chain A and (resid 11:26 or resid 29:30 or resid...AA280280
111ILEILEHOHHOH(chain A and (resid 11:26 or resid 29:30 or resid...AA - L11 - 50111
112ILEILEHOHHOH(chain A and (resid 11:26 or resid 29:30 or resid...AA - L11 - 50111
113ILEILEHOHHOH(chain A and (resid 11:26 or resid 29:30 or resid...AA - L11 - 50111
114ILEILEHOHHOH(chain A and (resid 11:26 or resid 29:30 or resid...AA - L11 - 50111
21ILEILEILEILE(chain B and ((resid 11 and (name N or name...BB1111
22ILEILEPTYPTY(chain B and ((resid 11 and (name N or name...BB - J11 - 40111
23ILEILEPTYPTY(chain B and ((resid 11 and (name N or name...BB - J11 - 40111
24ILEILEPTYPTY(chain B and ((resid 11 and (name N or name...BB - J11 - 40111
25ILEILEPTYPTY(chain B and ((resid 11 and (name N or name...BB - J11 - 40111

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catechol 1,2-dioxygenase


Mass: 34459.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_5824 / Plasmid: BuviA.00117.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JR51, catechol 1,2-dioxygenase

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Non-polymers , 6 types, 687 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.78 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Rigaku Reagents Screen JCSG+ well D6: 0.2 M Magnesium Chloride, 20% PEG 8000, 0.1 M Tris pH 8.5; 0.4 uL screen : 0.4 uL BuviA.00117.a.B1.PS02511 at 21.4 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→40.513 Å / Num. obs: 72445 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.15 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.72
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.75-1.80.5772.480.759199.8
1.8-1.840.4653.080.828199.8
1.84-1.90.3564.030.897199.7
1.9-1.960.2665.360.939199.8
1.96-2.020.2016.970.96199.9
2.02-2.090.1539.210.976199.6
2.09-2.170.13110.540.982199.6
2.17-2.260.1112.630.988199.6
2.26-2.360.08915.410.99199.5
2.36-2.470.07817.370.993199.5
2.47-2.610.06519.940.995199.4
2.61-2.770.05323.610.996199.6
2.77-2.960.04527.530.997199.3
2.96-3.20.03830.980.998199.5
3.2-3.50.03235.860.998199.4
3.5-3.910.03139.090.998199.2
3.91-4.520.02741.350.999199.3
4.52-5.530.02542.150.999199.3
5.53-7.830.025420.999198.6
7.830.02242.610.999193.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DMH

1dmh


Resolution: 1.75→40.513 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 1995 2.75 %
Rwork0.177 70446 -
obs0.1779 72441 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.58 Å2 / Biso mean: 32.0597 Å2 / Biso min: 11.22 Å2
Refinement stepCycle: final / Resolution: 1.75→40.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4577 0 113 686 5376
Biso mean--52.5 35.98 -
Num. residues----611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064851
X-RAY DIFFRACTIONf_angle_d0.8186591
X-RAY DIFFRACTIONf_chiral_restr0.053728
X-RAY DIFFRACTIONf_plane_restr0.006875
X-RAY DIFFRACTIONf_dihedral_angle_d10.4172910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2643X-RAY DIFFRACTION4.292TORSIONAL
12B2643X-RAY DIFFRACTION4.292TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.79370.26461340.246249835117100
1.7937-1.84220.26151460.244950085154100
1.8422-1.89650.30431510.237650155166100
1.8965-1.95770.23811350.223950165151100
1.9577-2.02760.26341430.212350045147100
2.0276-2.10880.23781460.195649915137100
2.1088-2.20480.22911370.194350365173100
2.2048-2.3210.23541340.18550455179100
2.321-2.46640.24131510.184850095160100
2.4664-2.65680.19651410.184750385179100
2.6568-2.92410.2371480.178950335181100
2.9241-3.34710.21221450.174150345179100
3.3471-4.21620.18981390.14545077521699
4.2162-40.52410.14811450.14945157530299
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)
14.4550.4952-1.64414.7627-1.98135.8151-0.2945-0.80060.23790.85290.08370.32430.0131-0.0250.18510.36030.1350.04770.3431-0.0850.202144.7431-16.36267.2808
21.3183-0.7176-0.15440.8314-0.30681.5388-0.0642-0.01560.0980.09870.07940.14370.0606-0.1366-0.01880.1311-0.044-0.01080.1012-0.01790.181841.1077-12.790947.5113
30.6746-0.2188-0.36491.7130.21920.53240.31440.37070.4049-0.2525-0.133-0.1346-0.2115-0.1989-0.11940.19780.07160.04720.25710.12310.340745.53873.062422.9097
40.9149-1.15480.32545.96320.19471.04830.34530.21620.6221-0.189-0.0111-0.6042-0.293-0.0417-0.21450.23110.04870.12260.20650.11570.422351.28663.257822.4048
51.252-0.4564-0.59211.1751-0.35771.79160.09330.30880.1981-0.1616-0.0046-0.05120.1138-0.2311-0.0880.143-0.003-0.03840.23240.02740.200343.2882-9.973827.5036
61.7537-1.2596-0.62271.3225-0.19712.19170.12710.37580.1903-0.2575-0.01650.22050.046-0.3493-0.08550.1331-0.0115-0.03530.29280.06930.269735.22-3.36428.8815
71.3982-0.4788-1.38130.6201-0.42833.22850.42310.56170.5618-0.4412-0.04560.0159-0.3969-0.4113-0.2640.28430.1310.00280.48130.18790.405937.21725.145217.9836
87.3026-3.5336-1.02976.37061.07455.99990.0957-0.22610.79940.07740.1534-0.2408-0.31550.2167-0.28370.146-0.0482-0.02880.09070.03920.343646.92653.457539.9438
95.1864-3.6871-0.99875.42860.73282.3569-0.14180.3069-0.1527-0.06740.04450.41050.2451-0.26490.1020.1676-0.12790.00580.23890.00490.260429.9256-16.428741.7281
101.9893-0.643-0.00320.7936-0.26140.7007-0.1349-0.03130.11590.13470.08530.06450.0994-0.07610.04490.1588-0.0297-0.01250.1068-0.02210.132244.5855-14.123649.5114
112.95390.50710.84152.9591-1.43072.1002-0.2668-0.731-0.67870.20970.08040.35730.50470.0150.13960.42910.06950.17250.28480.07550.305446.7288-33.756466.1334
121.4985-0.58420.0970.7860.04850.3721-0.4063-0.7016-0.61080.12710.1999-0.05790.25230.08860.2070.39320.1130.1270.31530.14720.315368.5495-36.459963.0973
131.26781.81480.17898.9043-2.59791.3959-0.3601-0.2761-0.6478-0.31940.1679-0.19290.35610.1330.21170.36590.09540.13240.20970.08140.375971.7281-36.649158.3655
142.8439-0.6852-0.15021.6564-0.50820.8801-0.3536-0.462-0.03450.1920.1951-0.0840.13680.21320.16490.29460.0706-0.00170.2588-0.00650.135563.4941-23.113263.1286
152.281-0.25560.70074.17010.74331.4091-0.3687-0.9035-0.29590.53330.11640.35830.21070.02250.15060.43350.13690.13260.46410.09110.212459.2256-31.573469.0478
160.3328-0.26960.19840.342-0.17890.1304-0.5459-0.9067-0.26430.48280.109-0.09370.28160.3958-0.08790.54680.32820.12250.83820.30670.236768.2902-33.812773.948
173.56583.17730.46647.7159-4.86315.7812-0.39880.0749-0.6343-0.07930.38580.260.724-0.35380.03360.44050.03470.13370.11050.00060.328553.1817-38.791655.8831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 38 )A11 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 115 )A39 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 178 )A116 - 178
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 199 )A179 - 199
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 241 )A200 - 241
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 272 )A242 - 272
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 307 )A273 - 307
8X-RAY DIFFRACTION8chain 'A' and (resid 308 through 320 )A308 - 320
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 38 )B11 - 38
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 90 )B39 - 90
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 115 )B91 - 115
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 178 )B116 - 178
13X-RAY DIFFRACTION13chain 'B' and (resid 179 through 199 )B179 - 199
14X-RAY DIFFRACTION14chain 'B' and (resid 200 through 241 )B200 - 241
15X-RAY DIFFRACTION15chain 'B' and (resid 242 through 263 )B242 - 263
16X-RAY DIFFRACTION16chain 'B' and (resid 264 through 301 )B264 - 301
17X-RAY DIFFRACTION17chain 'B' and (resid 302 through 320 )B302 - 320

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