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- PDB-5ve5: Crystal structure of persulfide dioxygenase rhodanese fusion prot... -

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Basic information

Entry
Database: PDB / ID: 5ve5
TitleCrystal structure of persulfide dioxygenase rhodanese fusion protein with rhodanese domain inactivating mutation (C314S) from Burkholderia phytofirmans in complex with glutathione
ComponentsBpPRF
KeywordsOXIDOREDUCTASE / TRANSFERASE / persulfide dioxygenase / rhodanese
Function / homology
Function and homology information


hydrogen sulfide metabolic process / sulfur dioxygenase activity / glutathione metabolic process / metal ion binding
Similarity search - Function
Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GLUTATHIONE / IMIDAZOLE / TRIETHYLENE GLYCOL / Beta-lactamase domain protein
Similarity search - Component
Biological speciesParaburkholderia phytofirmans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsMotl, N. / Skiba, M.A. / Smith, J.L. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112455 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008353 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation.
Authors: Motl, N. / Skiba, M.A. / Kabil, O. / Smith, J.L. / Banerjee, R.
History
DepositionApr 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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_struct_conn_angle / 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_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.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.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BpPRF
B: BpPRF
C: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,29615
Polymers124,8123
Non-polymers1,48412
Water3,405189
1
A: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2226
Polymers41,6041
Non-polymers6185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0034
Polymers41,6041
Non-polymers3993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0725
Polymers41,6041
Non-polymers4684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.503, 83.503, 547.609
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-404-

IMD

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 106 or resid 108...
21(chain B and (resid 0 through 106 or resid 108...
31(chain C and (resid 0 through 106 or resid 108 through 176 or resid 178 through 355))

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
11HISHISLEULEU(chain A and (resid 0 through 106 or resid 108...AA0 - 10620 - 126
12VALVALTYRTYR(chain A and (resid 0 through 106 or resid 108...AA108 - 176128 - 196
13GLYGLYLEULEU(chain A and (resid 0 through 106 or resid 108...AA178 - 230198 - 250
14PROPROGLYGLY(chain A and (resid 0 through 106 or resid 108...AA241 - 355261 - 375
21HISHISLEULEU(chain B and (resid 0 through 106 or resid 108...BB0 - 10620 - 126
22VALVALTYRTYR(chain B and (resid 0 through 106 or resid 108...BB108 - 176128 - 196
23GLYGLYLEULEU(chain B and (resid 0 through 106 or resid 108...BB178 - 230198 - 250
24PROPROGLYGLY(chain B and (resid 0 through 106 or resid 108...BB241 - 355261 - 375
31HISHISLEULEU(chain C and (resid 0 through 106 or resid 108 through 176 or resid 178 through 355))CC0 - 10620 - 126
32VALVALTYRTYR(chain C and (resid 0 through 106 or resid 108 through 176 or resid 178 through 355))CC108 - 176128 - 196
33GLYGLYGLYGLY(chain C and (resid 0 through 106 or resid 108 through 176 or resid 178 through 355))CC178 - 355198 - 375

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein BpPRF / Beta-lactamase domain protein


Mass: 41604.047 Da / Num. of mol.: 3 / Mutation: C314S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN) (bacteria)
Strain: DSM 17436 / LMG 22146 / PsJN / Gene: Bphyt_4191 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B2TEQ2, persulfide dioxygenase, thiosulfate sulfurtransferase

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Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole, pH 8.0, 0.12 M sodium chloride, 25% PEG8000, 5 mM GSH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.34→46.558 Å / Num. obs: 49143 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.645 % / Biso Wilson estimate: 49.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.134 / Χ2: 1.321 / Net I/σ(I): 10.98 / Num. measured all: 424862
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.34-2.499.1561.3931.7576940.9351.47699
2.49-2.669.0470.912.5472910.9660.965100
2.66-2.878.8760.5523.9568590.9810.58799.9
2.87-3.148.4280.3046.4863070.9890.32499.9
3.14-3.518.280.16610.8857780.9950.17799.9
3.51-4.058.8590.10718.4851320.9970.11399.9
4.05-4.958.4320.07625.6144160.9970.08199.3
4.95-6.967.6380.06526.3335150.9980.0798.9
6.96-46.5587.9150.0535.4921510.9980.05398

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5VE4

5ve4


Resolution: 2.35→43.656 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65
RfactorNum. reflection% reflection
Rfree0.252 2584 2.92 %
Rwork0.1973 --
obs0.1989 48680 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 221.53 Å2 / Biso mean: 76.6859 Å2 / Biso min: 36.41 Å2
Refinement stepCycle: final / Resolution: 2.35→43.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8136 0 74 189 8399
Biso mean--85.12 58.44 -
Num. residues----1046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138406
X-RAY DIFFRACTIONf_angle_d0.98311375
X-RAY DIFFRACTIONf_chiral_restr0.0591273
X-RAY DIFFRACTIONf_plane_restr0.0071496
X-RAY DIFFRACTIONf_dihedral_angle_d17.6164951
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4880X-RAY DIFFRACTION15.488TORSIONAL
12B4880X-RAY DIFFRACTION15.488TORSIONAL
13C4880X-RAY DIFFRACTION15.488TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.39520.3931440.35314798494299
2.3952-2.44410.33711380.329647984936100
2.4441-2.49720.39781460.3144730487699
2.4972-2.55530.32841450.302347694914100
2.5553-2.61920.34331460.27834828497499
2.6192-2.690.32751460.26714763490999
2.69-2.76920.31871430.269747444887100
2.7692-2.85850.30461450.25614726487199
2.8585-2.96070.3531450.248248124957100
2.9607-3.07920.34111430.234948104953100
3.0792-3.21930.27871400.229248044944100
3.2193-3.38890.33691480.229347274875100
3.3889-3.60120.24711440.195248054949100
3.6012-3.87910.23161460.179847624908100
3.8791-4.26910.22971490.157147774926100
4.2691-4.88620.17881490.145948034952100
4.8862-6.15330.23431320.15694759489199
6.1533-43.66390.17461350.15184773490899
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)
14.9927-0.855-1.03952.3242-1.74983.75340.01020.2141-0.1122-0.20420.05080.135-0.42390.0099-0.06880.7170.0385-0.07790.6450.05610.217421.338519.7641-41.0585
20.92480.17260.42530.5152-0.62411.6272-0.1508-0.19820.17150.44980.13470.0853-0.8828-0.3121-0.09951.1650.1829-0.03780.74840.14130.130618.051725.1678-31.6525
31.3539-0.57430.28050.9152-0.46321.51660.0597-0.13370.01860.226-0.1392-0.117-0.10470.28990.04970.8074-0.0171-0.05790.76590.13730.268830.49197.8366-29.1772
43.4905-2.5557-0.50354.99162.20151.2460.0973-0.4210.1041-0.0402-0.1239-0.5746-0.36620.4583-0.07591.2065-0.1458-0.09520.92550.10950.422138.173425.6162-26.3913
50.3682-0.07631.02880.0169-0.2192.8432-0.37360.01780.3780.7531-0.1968-0.0762-1.4210.65560.63151.4083-0.0494-0.19440.79660.07270.47121.951641.2416-44.6991
61.5001-0.42221.34072.113-2.23625.3907-0.3880.33980.71390.0094-0.1848-0.2127-0.87180.40080.52211.1382-0.0959-0.25160.6060.10010.538421.174247.3204-60.5338
72.81060.85-3.03431.8507-1.23243.34090.1580.04820.14470.0003-0.1359-0.0783-0.6633-0.00130.0531.0005-0.10450.04310.74390.09840.285830.668727.90496.3071
80.62760.20790.04660.1238-0.29582.1103-0.16220.30430.0342-0.41310.20880.01210.0814-0.10860.02171.0622-0.01810.03770.79670.12280.22528.877820.5691-1.7947
90.6729-0.6835-0.36040.78990.59570.8819-0.01690.2096-0.1184-0.41630.0389-0.37570.5390.3886-0.04150.9445-0.02860.0490.82380.16890.334135.472511.82614.1144
101.2214-0.218-0.34661.024-0.69392.01580.12450.1038-0.0428-0.1806-0.02740.0983-0.0137-0.1911-0.06640.8785-0.04160.00850.78260.12430.260320.762111.227517.3581
110.3275-0.43320.35290.9146-0.5680.41080.33590.42950.0358-0.07820.10690.2758-0.7759-1.0696-0.51351.2297-0.1463-0.15021.17070.31610.405911.425217.12531.2186
122.6531-0.63040.40084.0033-0.510.1069-0.30110.66850.914-0.4430.30720.09670.2145-0.17170.07051.11550.00780.08351.19150.3160.404627.936141.2725-9.1635
131.29720.6306-1.21241.9849-1.57993.35670.35840.30510.76950.48380.36960.725-1.3055-0.3506-0.36281.86930.28810.32841.14940.55990.977430.13461.7378-8.2397
140.79871.896-1.15254.5002-2.73611.66180.00930.72160.5578-0.46640.41760.6094-0.0713-0.7575-0.86741.61040.63750.58111.5180.7521.271217.9959.7469-8.2554
151.11991.2508-1.42712.5827-2.82235.73540.1603-0.01880.16620.12290.22680.39130.363-0.5374-0.10611.35580.24330.46771.0840.54390.861523.860253.3769-1.2698
166.30991.0688-0.60725.5622-1.35287.3541-0.12181.16090.95710.24980.92810.4627-1.0502-0.8964-0.61541.09280.0710.21911.11420.40290.613232.078554.2196-7.702
174.2576-1.2913-0.16714.5-1.13384.54850.30350.48530.46630.3562-0.3136-0.018-0.68720.4493-0.02951.0847-0.09330.13740.72960.0790.30424.943230.996124.6439
180.60390.64750.23061.1065-0.15580.54730.521-0.56610.40060.7669-0.22410.3399-0.9530.1828-0.05351.6648-0.2280.29371.00160.0140.42523.84236.878234.3506
190.59610.48310.49251.0045-0.85053.12180.6239-0.23580.53920.5454-0.08790.1627-1.35150.0719-0.39131.5717-0.12780.40790.86050.07610.575830.437547.14216.7619
200.72570.55040.25071.8278-0.31310.61860.10930.29380.41540.24540.22470.1868-0.5706-0.1577-0.29861.52160.12070.63491.05350.27070.74699.879843.959126.5769
212.11631.3276-0.54614.9542-2.25557.1339-0.11280.23450.35060.31060.49050.7622-0.2798-0.5037-0.40140.69580.03690.08090.92060.25470.42831.30668.979532.8234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 21 )A-1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 110 )A22 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 209 )A111 - 209
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 227 )A210 - 227
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 257 )A228 - 257
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 356 )A258 - 356
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 46 )B-1 - 46
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 84 )B47 - 84
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 110 )B85 - 110
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 209 )B111 - 209
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 227 )B210 - 227
12X-RAY DIFFRACTION12chain 'B' and (resid 228 through 263 )B228 - 263
13X-RAY DIFFRACTION13chain 'B' and (resid 264 through 288 )B264 - 288
14X-RAY DIFFRACTION14chain 'B' and (resid 289 through 309 )B289 - 309
15X-RAY DIFFRACTION15chain 'B' and (resid 310 through 329 )B310 - 329
16X-RAY DIFFRACTION16chain 'B' and (resid 330 through 355 )B330 - 355
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 21 )C0 - 21
18X-RAY DIFFRACTION18chain 'C' and (resid 22 through 110 )C22 - 110
19X-RAY DIFFRACTION19chain 'C' and (resid 111 through 208 )C111 - 208
20X-RAY DIFFRACTION20chain 'C' and (resid 209 through 245 )C209 - 245
21X-RAY DIFFRACTION21chain 'C' and (resid 246 through 356 )C246 - 356

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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