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- PDB-5ve3: Crystal structure of wild-type persulfide dioxygenase-rhodanese f... -

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Basic information

Entry
Database: PDB / ID: 5ve3
TitleCrystal structure of wild-type persulfide dioxygenase-rhodanese fusion protein from Burkholderia phytofirmans
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 ...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 superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Beta-lactamase domain protein
Similarity search - Component
Biological speciesParaburkholderia phytofirmans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.793 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 / Category: pdbx_audit_support / 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 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
B: BpPRF
A: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7014
Polymers82,5902
Non-polymers1122
Water9,206511
1
B: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3512
Polymers41,2951
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3512
Polymers41,2951
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.689, 108.333, 119.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BpPRF / Beta-lactamase domain protein


Mass: 41294.816 Da / Num. of mol.: 2
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
#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.: 511 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M zinc acetate, 0.1 M MES, pH 6.0, 10% PEG8000, 5 mM thiosulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 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: 1.79→43.598 Å / Num. obs: 78090 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12.386 % / Biso Wilson estimate: 28.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.124 / Χ2: 1.132 / Net I/σ(I): 14.55 / Num. measured all: 967249
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.79-1.99.9911.4291.3612201612530122120.6151.50597.5
1.9-2.0313.1090.9452.915414311760117590.8910.984100
2.03-2.1912.7910.5325.5114060210992109920.9660.554100
2.19-2.413.3820.329.0513535810115101150.9860.333100
2.4-2.6912.9950.19513.4119608920492040.9940.203100
2.69-3.113.3630.11621.76109160816981690.9970.121100
3.1-3.7912.3010.0734.6185467694869480.9980.073100
3.79-5.3411.7150.05444.3164070547054690.9990.056100
5.34-43.59811.4290.04546.3336825323432220.9990.04799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TP9

3tp9


Resolution: 1.793→43.598 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 3832 2.57 %
Rwork0.1606 145394 -
obs0.1616 77984 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.21 Å2 / Biso mean: 38.2323 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 1.793→43.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 2 511 5931
Biso mean--28.95 44.31 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165676
X-RAY DIFFRACTIONf_angle_d1.2667715
X-RAY DIFFRACTIONf_chiral_restr0.091866
X-RAY DIFFRACTIONf_plane_restr0.0091018
X-RAY DIFFRACTIONf_dihedral_angle_d14.3983393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7927-1.81540.36951210.37764701482286
1.8154-1.83930.36741420.350354175559100
1.8393-1.86450.31961400.319654305570100
1.8645-1.89110.31741430.30653345477100
1.8911-1.91930.31021460.299954635609100
1.9193-1.94930.29881420.290753665508100
1.9493-1.98130.30931410.279454545595100
1.9813-2.01540.29021430.240454285571100
2.0154-2.05210.29411400.224154115551100
2.0521-2.09150.27341440.212353775521100
2.0915-2.13420.23051400.193554045544100
2.1342-2.18060.21681450.183354255570100
2.1806-2.23140.23121440.173154035547100
2.2314-2.28720.23351420.16754525594100
2.2872-2.3490.21621360.158754045540100
2.349-2.41810.19041430.155453965539100
2.4181-2.49620.21761450.151553955540100
2.4962-2.58540.16431460.146254175563100
2.5854-2.68890.1821420.146454295571100
2.6889-2.81120.18621380.14954145552100
2.8112-2.95940.17831460.156353935539100
2.9594-3.14480.22961450.159154315576100
3.1448-3.38750.20931430.146754225565100
3.3875-3.72820.1661420.142353975539100
3.7282-4.26730.15061420.117354215563100
4.2673-5.37480.12221430.109954125555100
5.3748-43.6110.16631480.136853985546100
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)
10.7481-0.07580.19242.6749-0.77251.84210.07040.0576-0.1331-0.2068-0.0160.07560.2530.0148-0.05130.2391-0.0022-0.02480.2265-0.0170.24250.320728.788913.8198
26.95324.1673-0.16788.21210.2486.04740.07370.4061-0.0462-0.1945-0.223-0.88110.4670.60450.14740.35510.14690.00360.42730.04630.34815.111527.16873.4813
31.828-1.74883.5261.617-3.28316.86020.36450.4111-0.06-0.7009-0.28130.1250.81870.7412-0.03730.40050.0481-0.00930.3393-0.02290.275114.24458.096426.6787
46.75576.72285.3258.495.76234.3220.1069-0.1193-0.20830.4473-0.05-0.36990.21580.0734-0.10390.29440.0803-0.03790.26790.03590.308321.34670.508645.6309
58.46113.0531-0.98895.6767-0.62274.0475-0.04690.4150.0222-0.13960.0132-0.41660.00960.38010.04240.21350.0296-0.04290.22730.01760.207222.23416.256740.7767
68.9836-6.6375-1.44026.5590.66784.7740.10170.0323-0.20940.0502-0.03650.2293-0.19590.0005-0.08360.2054-0.0456-0.02290.1270.0180.153.872639.760730.6523
78.0791-1.62263.30621.3594-1.0753.7781-0.13960.13060.11590.23770.0522-0.0403-0.43120.11510.08630.3487-0.0379-0.00960.1509-0.00920.2057.08947.090333.2078
87.8949-4.91625.63338.8745-8.22848.9882-0.00560.19310.38440.34440.0566-0.2863-0.55490.1567-0.08110.4532-0.0498-0.04520.174-0.07960.236210.763652.231840.2154
91.2306-0.70020.68462.4992-0.482.2996-0.0424-0.1361-0.04780.35460.11990.0368-0.1781-0.0244-0.08160.2594-0.01120.01820.19340.01580.18086.988833.762944.1029
102.77472.0660.26885.566-1.55422.1837-0.01540.0046-0.29530.0308-0.058-0.53840.00460.25050.08820.2680.01380.00460.2692-0.01780.225716.904925.795643.3152
110.10020.5466-0.6063.5116-4.74246.80190.0871-0.02420.02550.43440.0061-0.1063-0.72750.4085-0.01430.2997-0.05350.04560.3037-0.02830.287613.210857.261821.8272
125.6276-1.1075-1.97613.13790.67694.48870.0928-0.04880.2897-0.1784-0.0071-0.1174-0.16390.1732-0.06420.2542-0.03460.02990.18710.02780.206311.687661.664.6975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid -2 through 209 )B-2 - 209
2X-RAY DIFFRACTION2chain 'B' and (resid 210 through 227 )B210 - 227
3X-RAY DIFFRACTION3chain 'B' and (resid 228 through 257 )B228 - 257
4X-RAY DIFFRACTION4chain 'B' and (resid 258 through 293 )B258 - 293
5X-RAY DIFFRACTION5chain 'B' and (resid 294 through 353 )B294 - 353
6X-RAY DIFFRACTION6chain 'A' and (resid -2 through 21 )A-2 - 21
7X-RAY DIFFRACTION7chain 'A' and (resid 22 through 66 )A22 - 66
8X-RAY DIFFRACTION8chain 'A' and (resid 67 through 84 )A67 - 84
9X-RAY DIFFRACTION9chain 'A' and (resid 85 through 183 )A85 - 183
10X-RAY DIFFRACTION10chain 'A' and (resid 184 through 227 )A184 - 227
11X-RAY DIFFRACTION11chain 'A' and (resid 228 through 257 )A228 - 257
12X-RAY DIFFRACTION12chain 'A' and (resid 258 through 353 )A258 - 353

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