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- PDB-5ve4: Crystal structure of persulfide dioxygenase-rhodanese fusion prot... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ve4
TitleCrystal structure of persulfide dioxygenase-rhodanese fusion protein with rhodanese domain inactivating mutation (C314S) 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
: / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Beta-lactamase domain protein
Similarity search - Component
Biological speciesParaburkholderia phytofirmans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)125,35312
Polymers124,8123
Non-polymers5419
Water1,58588
1
A: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8945
Polymers41,6041
Non-polymers2904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7644
Polymers41,6041
Non-polymers1603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BpPRF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6953
Polymers41,6041
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.504, 84.504, 549.379
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-531-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:144 or resseq 147:176 or resseq...
21(chain B and (resseq 1:144 or resseq 147:176 or resseq...
31(chain C and (resseq 1:144 or resseq 147:176 or resseq...

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
11METMETASPASP(chain A and (resseq 1:144 or resseq 147:176 or resseq...AA1 - 14421 - 164
12ARGARGTYRTYR(chain A and (resseq 1:144 or resseq 147:176 or resseq...AA147 - 176167 - 196
13GLYGLYGLUGLU(chain A and (resseq 1:144 or resseq 147:176 or resseq...AA178 - 187198 - 207
14ARGARGGLYGLY(chain A and (resseq 1:144 or resseq 147:176 or resseq...AA189 - 229209 - 249
15PROPROASNASN(chain A and (resseq 1:144 or resseq 147:176 or resseq...AA241 - 354261 - 374
21METMETASPASP(chain B and (resseq 1:144 or resseq 147:176 or resseq...BB1 - 14421 - 164
22ARGARGTYRTYR(chain B and (resseq 1:144 or resseq 147:176 or resseq...BB147 - 176167 - 196
23GLYGLYGLUGLU(chain B and (resseq 1:144 or resseq 147:176 or resseq...BB178 - 187198 - 207
24ARGARGGLYGLY(chain B and (resseq 1:144 or resseq 147:176 or resseq...BB189 - 229209 - 249
25PROPROASNASN(chain B and (resseq 1:144 or resseq 147:176 or resseq...BB241 - 354261 - 374
31METMETASPASP(chain C and (resseq 1:144 or resseq 147:176 or resseq...CC1 - 14421 - 164
32ARGARGTYRTYR(chain C and (resseq 1:144 or resseq 147:176 or resseq...CC147 - 176167 - 196
33GLYGLYGLUGLU(chain C and (resseq 1:144 or resseq 147:176 or resseq...CC178 - 187198 - 207
34ARGARGGLYGLY(chain C and (resseq 1:144 or resseq 147:176 or resseq...CC189 - 229209 - 249
35PROPROASNASN(chain C and (resseq 1:144 or resseq 147:176 or resseq...CC241 - 354261 - 374

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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, 97 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
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

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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: Oct 9, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.65→46.876 Å / Num. obs: 35549 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.592 % / Biso Wilson estimate: 62.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.135 / Χ2: 1.207 / Net I/σ(I): 11.59 / Num. measured all: 305449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.818.651.2291.955560.9061.30699.9
2.81-39.1360.7493.1552380.9640.793100
3-3.248.9310.433549470.9780.46100
3.24-3.548.5880.2278.3245640.9930.24299.9
3.54-3.968.3250.13313.2641500.9950.14299.9
3.96-4.578.6180.0920.3337110.9960.09699.8
4.57-5.588.6360.07723.6332130.9970.08299.8
5.58-7.847.870.07224.0925610.9970.07799.7
7.84-46.8767.2830.04733.5916090.9980.0598.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VE3

5ve3


Resolution: 2.65→46.876 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.62
RfactorNum. reflection% reflection
Rfree0.2671 1859 2.93 %
Rwork0.232 --
obs0.233 35305 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 186.88 Å2 / Biso mean: 82.0371 Å2 / Biso min: 20.49 Å2
Refinement stepCycle: final / Resolution: 2.65→46.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8131 0 24 88 8243
Biso mean--65.93 45.55 -
Num. residues----1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078357
X-RAY DIFFRACTIONf_angle_d0.69311314
X-RAY DIFFRACTIONf_chiral_restr0.0461267
X-RAY DIFFRACTIONf_plane_restr0.0041486
X-RAY DIFFRACTIONf_dihedral_angle_d16.8434945
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4831X-RAY DIFFRACTION10.802TORSIONAL
12B4831X-RAY DIFFRACTION10.802TORSIONAL
13C4831X-RAY DIFFRACTION10.802TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.72170.50391510.40544730488199
2.7217-2.80170.41921430.371947054848100
2.8017-2.89220.3851380.340647124850100
2.8922-2.99550.35871490.326147634912100
2.9955-3.11540.3491400.315947704910100
3.1154-3.25720.35651400.30247544894100
3.2572-3.42890.33271440.287546994843100
3.4289-3.64360.25191490.262247424891100
3.6436-3.92480.24081440.229247324876100
3.9248-4.31950.21971450.192847564901100
4.3195-4.9440.19571490.172747674916100
4.944-6.22660.27111310.193447494880100
6.2266-46.88330.21741360.183747644900100
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)
16.4866-3.88293.16723.5464-0.37898.2219-0.08220.3889-0.1167-0.41120.08010.2191-0.4740.0113-0.0270.7685-0.0467-0.11630.58130.17280.528721.028919.576-41.3104
22.75711.08621.97864.6056-1.02467.7387-0.0564-0.07420.58560.82590.03210.2411-1.3763-0.5083-0.02261.02790.0633-0.04040.67650.07270.567318.500627.8412-35.0699
34.22331.40254.32813.56933.55627.6318-0.2629-0.72730.12820.16770.09920.3333-1.0252-1.06850.19730.85420.0870.06870.95740.18790.557714.021418.4869-25.0869
43.2536-1.0610.76262.8684-1.41284.1649-0.0612-0.2788-0.03490.2768-0.0757-0.2495-0.08930.56210.10540.6557-0.0662-0.05010.76710.17130.54629.48347.5665-29.2585
58.9042-6.9976-0.15349.40660.33674.13180.334-0.10440.54230.5257-0.399-2.0582-0.74710.84550.25080.9706-0.229-0.21760.99750.25291.02737.103225.6387-26.3152
60.071-0.8560.71277.2625-5.85014.6676-0.6499-0.37740.49550.42580.31910.3239-1.7809-0.27020.54521.29480.0012-0.29340.87150.0350.950518.537243.1601-46.8894
75.9636-2.38120.06011.0177-0.27143.4394-0.17880.41361.551-0.50360.0656-0.3278-1.07870.43490.43291.4925-0.218-0.42390.77180.37951.063518.4650.1027-66.5859
86.6672-0.6194-0.22791.64530.35315.3416-0.3373-0.23751.041-0.3001-0.2211-0.9282-1.13911.03060.61731.2878-0.2454-0.26360.97940.34881.121726.802548.2663-62.0874
91.9093-0.35-0.5913.20540.05142.91310.0572-0.05750.71950.1721-0.4928-0.1607-0.89470.16410.44141.2618-0.2181-0.34450.83820.16080.893518.746344.1516-59.7001
103.35332.6007-1.38534.4278-2.20195.9364-0.05710.12310.1552-0.46010.1075-0.0822-0.1230.1402-0.04430.7774-0.0336-0.00570.75530.15940.52328.771324.9162.6788
112.81480.9399-2.81943.6828-1.86615.4828-0.12250.0913-0.0929-0.22560.0691-0.03210.2645-0.13460.06720.7240.0194-0.00670.76190.19970.522824.087712.155114.247
122.96022.3956-1.99581.9215-1.57183.385-0.15480.60180.6523-0.73650.93010.9020.5867-1.0029-0.74680.9599-0.0047-0.02991.13040.30150.752312.64617.47262.9104
130.87470.4778-0.35648.4063-2.41955.26140.36210.51460.91930.27410.31230.6921-1.4295-0.8476-0.64431.19590.16930.23151.11650.42251.137526.34955.0974-7.0885
146.8324-3.92727.6388.1703-5.75029.29560.20490.15810.91490.189-0.6415-0.3388-0.19560.6570.39421.0024-0.07780.15230.97690.16370.615523.88931.223524.5168
152.43070.5735-1.32254.5754-0.65495.78380.5976-0.60210.34651.2637-0.27210.2835-1.59480.3566-0.3271.4478-0.22640.20791.02230.0170.676524.527639.065931.0686
166.8049-5.78892.66735.7679-0.74153.90190.6221-0.43020.5660.114-0.10890.3489-2.0972-0.1187-0.45911.9717-0.25150.42730.93420.12411.007626.247556.104819.0742
178.30052.79860.00343.53770.33460.19740.65770.1710.92110.0568-0.4230.2731-0.8050.2673-0.29011.2314-0.27370.13490.93690.09870.634530.289739.939416.2815
183.6351.9856-5.16777.8582-2.18187.40250.78840.81941.22130.05720.02970.3583-1.5061-0.5903-0.90641.3346-0.1130.11030.83060.06490.857824.67451.369611.3508
191.46231.9914-2.40726.7319-3.1143.27670.3954-0.2950.13931.0477-0.23470.5768-1.0540.0022-0.19111.25080.11490.20180.96680.18670.82996.799726.095536.6054
204.1161.18660.59416.6416-0.17770.2847-0.09030.47160.0441-0.2190.55431.03180.1927-1.1054-0.46220.72280.05020.05951.18870.43210.8428-3.60984.208431.0382
218.7545-1.6351-0.24055.44470.79179.0416-0.26520.10170.43250.20440.44530.4483-0.5568-0.7245-0.27410.66690.03880.09250.88520.28670.72341.350110.413932.6629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 21 )A0 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 81 )A22 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 110 )A82 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 209 )A111 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 227 )A210 - 227
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 263 )A228 - 263
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 293 )A264 - 293
8X-RAY DIFFRACTION8chain 'A' and (resid 294 through 317 )A294 - 317
9X-RAY DIFFRACTION9chain 'A' and (resid 318 through 356 )A318 - 356
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 84 )B-1 - 84
11X-RAY DIFFRACTION11chain 'B' and (resid 85 through 199 )B85 - 199
12X-RAY DIFFRACTION12chain 'B' and (resid 200 through 245 )B200 - 245
13X-RAY DIFFRACTION13chain 'B' and (resid 246 through 354 )B246 - 354
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 21 )C0 - 21
15X-RAY DIFFRACTION15chain 'C' and (resid 22 through 142 )C22 - 142
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 159 )C143 - 159
17X-RAY DIFFRACTION17chain 'C' and (resid 160 through 183 )C160 - 183
18X-RAY DIFFRACTION18chain 'C' and (resid 184 through 220 )C184 - 220
19X-RAY DIFFRACTION19chain 'C' and (resid 221 through 263 )C221 - 263
20X-RAY DIFFRACTION20chain 'C' and (resid 264 through 303 )C264 - 303
21X-RAY DIFFRACTION21chain 'C' and (resid 304 through 356 )C304 - 356

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