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- PDB-5vdn: 1.55 Angstrom Resolution Crystal Structure of Glutathione Reducta... -

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Basic information

Entry
Database: PDB / ID: 5vdn
Title1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis in Complex with FAD
ComponentsGlutathione oxidoreductase
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutathione Reductase / FAD
Function / homology
Function and homology information


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 / FLAVIN-ADENINE DINUCLEOTIDE / : / Glutathione oxidoreductase
Similarity search - Component
Biological speciesYersinia pestis KIM10+ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis in Complex with FAD.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 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_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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
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 oxidoreductase
B: Glutathione oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,98010
Polymers100,7862
Non-polymers2,1948
Water22,9151272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 1GES
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-66 kcal/mol
Surface area33960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.844, 125.844, 124.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-1225-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glutathione oxidoreductase


Mass: 50393.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis KIM10+ (bacteria) / Gene: gor / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q8CZL0, glutathione-disulfide reductase
#4: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
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 , 4 types, 1278 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 10.0 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B6), 0.49M Sodium phosphate, 0.91M Potassium phosphate; Cryo: Screen : 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: Mar 28, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 161196 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rsym value: 0.06 / Χ2: 1.003 / Net I/σ(I): 25.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8068 / CC1/2: 0.729 / Rpim(I) all: 0.319 / Rsym value: 0.721 / Χ2: 1.013 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GES

1ges


Resolution: 1.55→29.94 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.249 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16456 7895 4.9 %RANDOM
Rwork0.14471 ---
obs0.14567 153253 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.55→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6870 0 144 1272 8286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197689
X-RAY DIFFRACTIONr_bond_other_d0.0010.027060
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.96710528
X-RAY DIFFRACTIONr_angle_other_deg0.873316413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.74951001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86624.468329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.136151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6261539
X-RAY DIFFRACTIONr_chiral_restr0.0930.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.028776
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021525
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_it0.8621.3823875
X-RAY DIFFRACTIONr_mcbond_other0.8621.3823874
X-RAY DIFFRACTIONr_mcangle_it1.3532.0724919
X-RAY DIFFRACTIONr_mcangle_other1.3532.0734920
X-RAY DIFFRACTIONr_scbond_it1.8661.6713814
X-RAY DIFFRACTIONr_scbond_other1.8661.6713814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8932.4075610
X-RAY DIFFRACTIONr_long_range_B_refined5.85219.8369250
X-RAY DIFFRACTIONr_long_range_B_other5.35617.8968751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 570 -
Rwork0.229 11150 -
obs--98.51 %
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)
10.2678-0.2465-0.17511.13940.51070.3968-0.0205-0.0298-0.03450.14420.00610.07030.0406-0.0370.01440.04160.01440.0070.03020.00760.01060.274438.6754-4.5436
20.46860.03920.06190.33510.05840.7379-0.00260.0112-0.01220.0031-0.00140.02160.0081-0.16590.0040.008-0.0011-0.01130.0660.00270.02-8.762233.6959-28.4554
31.09950.11770.05680.88610.47131.01320.01840.04480.0966-0.0894-0.00170.0234-0.14410.0485-0.01670.04920.01220.0090.0160.00430.01392.237856.8502-8.9263
40.2762-0.1270.2330.8981-0.04770.3634-0.0030.03660.0053-0.0466-0.0176-0.0212-0.02640.02390.02060.024-0.00060.00290.03560.00690.009918.616940.749-30.6235
51.14250.2574-0.53930.2726-0.09930.4038-0.05550.1321-0.08-0.05090.0395-0.00580.0518-0.02080.01590.02060.0009-0.00260.0518-0.00950.011133.35319.5808-37.4485
60.3806-0.0845-0.03050.5922-0.06950.8197-0.0112-0.0056-0.02890.01060.0085-0.00010.15430.07750.00270.05050.0236-0.00720.02020.00780.01833.56859.2494-13.5306
70.8535-0.0208-0.37331.1689-0.27580.98410.0198-0.08330.03290.051-0.0024-0.0978-0.11290.1059-0.01740.0145-0.00770.00070.054-0.00890.014148.117330.3559-33.0494
80.84930.20260.16190.3242-0.1550.359-0.0118-0.05250.01710.0303-0.00640.007-0.03570.00870.01810.03170.0056-0.00350.0264-0.00470.009125.979936.4939-11.3562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 153
2X-RAY DIFFRACTION2A154 - 273
3X-RAY DIFFRACTION3A274 - 346
4X-RAY DIFFRACTION4A347 - 460
5X-RAY DIFFRACTION5B12 - 153
6X-RAY DIFFRACTION6B154 - 273
7X-RAY DIFFRACTION7B274 - 346
8X-RAY DIFFRACTION8B347 - 460

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