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- PDB-5v36: 1.88 Angstrom Resolution Crystal Structure of Glutathione Reducta... -

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Basic information

Entry
Database: PDB / ID: 5v36
Title1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD
ComponentsGlutathione reductase
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutathione Reductase / FAD
Function / homology
Function and homology information


glutathione-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-fructopyranose / BETA-MERCAPTOETHANOL / FLAVIN-ADENINE DINUCLEOTIDE / Glutathione reductase
Similarity search - Component
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione reductase
B: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,38751
Polymers98,6152
Non-polymers5,77249
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19470 Å2
ΔGint-544 kcal/mol
Surface area33490 Å2
MethodPISA
2
A: Glutathione reductase
B: Glutathione reductase
hetero molecules

A: Glutathione reductase
B: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,773102
Polymers197,2304
Non-polymers11,54498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area40750 Å2
ΔGint-1102 kcal/mol
Surface area65170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.333, 126.333, 247.876
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Glutathione reductase


Mass: 49307.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: gshR, SMU_838 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic
References: UniProt: Q8DUR5, adenosylhomocysteinase, glutathione-disulfide reductase
#8: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1082 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 8.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1.mM FAD; Screen: Classics II (A5), 2M Ammonium sulfate, 0.1 HEPES (pH 7.5); Cryo: 4M Ammonium sulfate : 50% Sucrose (1:1)

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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 23, 2017 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 95700 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.02 / Rsym value: 0.076 / Χ2: 1.003 / Net I/σ(I): 35.2
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 14 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4685 / CC1/2: 0.888 / Rpim(I) all: 0.21 / Rsym value: 0.775 / Χ2: 0.997 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U1O

5u1o


Resolution: 1.88→29.81 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.126 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17048 4741 5 %RANDOM
Rwork0.14286 ---
obs0.14424 90417 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.111 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---1.03 Å2
Refinement stepCycle: 1 / Resolution: 1.88→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 329 1034 8277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197886
X-RAY DIFFRACTIONr_bond_other_d0.0010.027037
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.98310782
X-RAY DIFFRACTIONr_angle_other_deg0.8493.00116353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.86551010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83824.435345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.103151263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8131537
X-RAY DIFFRACTIONr_chiral_restr0.0830.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.028947
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021604
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.9463890
X-RAY DIFFRACTIONr_mcbond_other0.9391.9453889
X-RAY DIFFRACTIONr_mcangle_it1.4022.9134950
X-RAY DIFFRACTIONr_mcangle_other1.4022.9144951
X-RAY DIFFRACTIONr_scbond_it1.8382.3623996
X-RAY DIFFRACTIONr_scbond_other1.8372.3623996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7563.4465833
X-RAY DIFFRACTIONr_long_range_B_refined5.92425.8079291
X-RAY DIFFRACTIONr_long_range_B_other5.65324.6789006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 338 -
Rwork0.184 6531 -
obs--99.74 %
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)
11.76160.30630.28823.19040.37261.7112-0.05510.2130.0252-0.412-0.0073-0.09040.0554-0.00110.06230.1141-0.0398-0.00190.09610.03570.021415.682782.1498-6.387
21.8825-0.22060.86510.15140.03550.7472-0.07390.01040.2031-0.03470.0213-0.0542-0.1329-0.01640.05260.0895-0.03390.00370.07210.04810.103540.092396.1411.0238
30.71640.61750.56241.21250.44141.2151-0.09480.08940.049-0.20690.08110.0546-0.1131-0.08740.01370.0629-0.0094-0.01570.08170.05340.050915.024291.65880.6294
40.9558-0.48270.15540.9255-0.30111.3230.012-0.04320.13170.03510.03360.0463-0.2281-0.0495-0.04550.0645-0.02270.00870.04760.01040.045726.8359101.093726.4315
50.34870.15890.13190.30880.0020.55830.0331-0.05540.0043-0.0229-0.03910.05130.0288-0.09840.00610.0405-0.0235-0.01630.07050.03310.045616.512183.162813.2792
63.18692.1729-0.81462.427-0.10070.49840.0731-0.1977-0.00310.1388-0.0595-0.00290.01910.0113-0.01360.0959-0.0384-0.03260.1350.05590.051934.72977.108533.9041
70.73960.0498-0.02961.0790.2810.52620.0012-0.0954-0.06790.0093-0.0182-0.00660.0494-0.02260.0170.0547-0.034-0.02040.0820.06360.052237.149571.982725.7651
83.0690.4066-0.38633.0913-0.82561.7531-0.0162-0.27710.08540.3234-0.03040.0048-0.05960.06220.04660.07620.01050.00830.04930.0070.012759.905660.966144.5634
90.4599-0.17890.0380.6196-0.18220.2856-0.0184-0.03080.06260.0560.0061-0.0376-0.00410.08040.01230.0364-0.0139-0.00010.05050.00830.030962.467375.998630.4177
101.18730.08690.31830.61070.22420.45760.01320.02170.035-0.04450.0269-0.01420.0460.0048-0.040.0859-0.03880.00480.05510.03170.045962.670777.018610.0167
112.1397-0.18750.00371.45630.0081.12340.00050.03440.0794-0.216-0.0056-0.09580.09550.17150.0050.0821-0.01520.02340.07320.01670.029775.570777.01959.2802
121.71910.24030.03591.2567-0.23091.1466-0.02530.0491-0.0742-0.09560.02230.05220.1463-0.01310.00310.07480.00830.00960.0390.03170.036157.650254.831131.0968
130.7460.3431-0.37892.41870.0510.292-0.00850.03-0.0543-0.194-0.0095-0.0410.00450.00390.0180.0872-0.0372-0.02130.06410.04290.051244.614269.73427.574
140.75410.2927-0.04941.42120.17860.55220.0212-0.0097-0.0437-0.1154-0.02490.07940.0296-0.04330.00360.0724-0.0227-0.0240.05850.05080.057835.557171.147613.4778
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 37
2X-RAY DIFFRACTION2A38 - 98
3X-RAY DIFFRACTION3A99 - 161
4X-RAY DIFFRACTION4A162 - 249
5X-RAY DIFFRACTION5A250 - 360
6X-RAY DIFFRACTION6A361 - 401
7X-RAY DIFFRACTION7A402 - 450
8X-RAY DIFFRACTION8B0 - 37
9X-RAY DIFFRACTION9B38 - 161
10X-RAY DIFFRACTION10B162 - 220
11X-RAY DIFFRACTION11B221 - 263
12X-RAY DIFFRACTION12B264 - 337
13X-RAY DIFFRACTION13B338 - 410
14X-RAY DIFFRACTION14B411 - 450

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