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- PDB-5n0j: Structure of a novel oxidoreductase from Gloeobacter violaceus -

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Basic information

Entry
Database: PDB / ID: 5n0j
TitleStructure of a novel oxidoreductase from Gloeobacter violaceus
ComponentsGll2934 protein
KeywordsOXIDOREDUCTASE / flavoprotein
Function / homologythioredoxin-disulfide reductase (NADPH) activity / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / cell redox homeostasis / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Gll2934 protein
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsBuey, R.M. / Galindo-Trigo, S. / de Pereda, J.M. / Balsera, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unprecedented pathway of reducing equivalents in a diflavin-linked disulfide oxidoreductase.
Authors: Buey, R.M. / Arellano, J.B. / Lopez-Maury, L. / Galindo-Trigo, S. / Velazquez-Campoy, A. / Revuelta, J.L. / de Pereda, J.M. / Florencio, F.J. / Schurmann, P. / Buchanan, B.B. / Balsera, M.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gll2934 protein
B: Gll2934 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,25021
Polymers77,6672
Non-polymers4,58319
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-210 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.842, 143.325, 265.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Gll2934 protein


Mass: 38833.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: gll2934 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NCP4
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.54 Å3/Da / Density % sol: 65.23 %
Description: Crystals were yellow but turned transparent after soaking them in a solution with 0.1 M reduced glutathione for a few minutes (up to 5 minutes)
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Li2SO4 0.1 M HEPES, pH 7.5 Crystals were soaked for 5 min in a solution of mother liquor plus 0.1 M reduced Glutathione, immersed in a solution of mother liquor containing 25% Ethylene ...Details: 1.5 M Li2SO4 0.1 M HEPES, pH 7.5 Crystals were soaked for 5 min in a solution of mother liquor plus 0.1 M reduced Glutathione, immersed in a solution of mother liquor containing 25% Ethylene glycol and immediately flash-frozen in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.949→49.73 Å / Num. obs: 80406 / % possible obs: 99.03 % / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.19
Reflection shellResolution: 1.949→2.019 Å / Redundancy: 10 % / Rmerge(I) obs: 2.84 / Mean I/σ(I) obs: 0.88 / CC1/2: 0.472 / % possible all: 95.71

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRI

5jri


Resolution: 1.949→49.728 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 3961 4.94 %
Rwork0.2017 --
obs0.2033 80159 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→49.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 287 341 5307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115135
X-RAY DIFFRACTIONf_angle_d1.1057036
X-RAY DIFFRACTIONf_dihedral_angle_d13.9712824
X-RAY DIFFRACTIONf_chiral_restr0.061777
X-RAY DIFFRACTIONf_plane_restr0.007849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9487-1.97250.47311450.4622433X-RAY DIFFRACTION90
1.9725-1.99740.461490.43532669X-RAY DIFFRACTION98
1.9974-2.02370.43241270.39722675X-RAY DIFFRACTION98
2.0237-2.05150.39361430.36722686X-RAY DIFFRACTION99
2.0515-2.08080.37391530.35432684X-RAY DIFFRACTION100
2.0808-2.11180.32011500.32412688X-RAY DIFFRACTION100
2.1118-2.14480.35231300.31462739X-RAY DIFFRACTION99
2.1448-2.180.34721320.30462695X-RAY DIFFRACTION100
2.18-2.21760.33741590.28372718X-RAY DIFFRACTION100
2.2176-2.25790.31121500.2752688X-RAY DIFFRACTION100
2.2579-2.30130.28951290.26572729X-RAY DIFFRACTION100
2.3013-2.34830.29751440.25212751X-RAY DIFFRACTION100
2.3483-2.39940.25661470.23932700X-RAY DIFFRACTION100
2.3994-2.45520.28561370.22162709X-RAY DIFFRACTION100
2.4552-2.51660.26671480.2122776X-RAY DIFFRACTION100
2.5166-2.58460.22141430.2072667X-RAY DIFFRACTION100
2.5846-2.66070.25421430.2062718X-RAY DIFFRACTION99
2.6607-2.74650.25021340.19432770X-RAY DIFFRACTION100
2.7465-2.84470.22991430.18732724X-RAY DIFFRACTION100
2.8447-2.95860.20441330.19292744X-RAY DIFFRACTION100
2.9586-3.09320.24051330.18892744X-RAY DIFFRACTION100
3.0932-3.25620.21561370.18062782X-RAY DIFFRACTION100
3.2562-3.46020.19461210.17272760X-RAY DIFFRACTION99
3.4602-3.72730.21161600.15752726X-RAY DIFFRACTION99
3.7273-4.10220.17081570.14462752X-RAY DIFFRACTION99
4.1022-4.69540.17231510.13252772X-RAY DIFFRACTION99
4.6954-5.91420.18221380.16382788X-RAY DIFFRACTION98
5.9142-49.74460.23861250.22542911X-RAY DIFFRACTION97
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)
11.3936-0.1512-0.73730.85860.65250.9804-0.0605-0.53870.12650.18710.1081-0.16460.25250.40270.00120.44650.0444-0.04020.6671-0.12180.411778.5836161.6015307.4263
21.39220.16420.21990.89430.61271.26960.0106-0.05610.08880.0627-0.0002-0.03040.06740.11940.00040.3845-0.0107-0.00070.2864-0.07030.361474.686154.9276276.6846
30.7479-0.2763-0.16540.54620.70041.2704-0.0968-0.371-0.02630.16130.01440.03650.31720.17930.01490.44830.0157-0.00340.5018-0.03420.450675.8295154.111292.8153
40.3906-0.291-0.09510.39560.1360.1378-0.1078-0.68240.03630.01430.0930.08270.5699-0.26350.07450.455-0.02080.01860.6276-0.09820.383463.7314161.8791312.433
52.17170.8669-0.31812.19480.49620.2570.1210.63720.3678-0.6493-0.14780.1195-0.7913-0.53310.23540.54550.2037-0.03610.7204-0.12910.417249.6631175.1336282.2275
61.2295-0.0671-0.2330.41090.83432.82120.0232-0.38960.2973-0.0177-0.15420.0907-0.1821-0.4234-0.02420.39760.0317-0.00160.6532-0.23160.521352.1946177.9261307.8576
71.45690.37430.631.1480.04980.3718-0.03810.1564-0.003-0.0523-0.18220.10510.1323-0.1052-0.0180.37090.0121-0.00390.531-0.08330.432958.4933161.6403284.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 140 )
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 219 )
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 296 )
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 318 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 27 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 282 )
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 334 )

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