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- PDB-6b4o: 1.73 Angstrom Resolution Crystal Structure of Glutathione Reducta... -

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Basic information

Entry
Database: PDB / ID: 6b4o
Title1.73 Angstrom Resolution Crystal Structure of Glutathione Reductase from Enterococcus faecalis in Complex with FAD
ComponentsGlutathione reductase
KeywordsHYDROLASE / 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 / cellular response to oxidative stress / metal ion binding / cytosol
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 ...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
FLAVIN-ADENINE DINUCLEOTIDE / Glutathione reductase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMinasov, G. / Warwzak, Z. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionSep 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3Feb 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
C: Glutathione reductase
D: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,89139
Polymers198,7724
Non-polymers4,11935
Water34,5171916
1
A: Glutathione reductase
B: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,45820
Polymers99,3862
Non-polymers2,07118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-216 kcal/mol
Surface area34400 Å2
MethodPISA
2
C: Glutathione reductase
D: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,43319
Polymers99,3862
Non-polymers2,04717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-198 kcal/mol
Surface area34570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.686, 152.613, 98.531
Angle α, β, γ (deg.)90.00, 94.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione reductase


Mass: 49693.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: V583 / Gene: gor / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q82Z09, adenosylhomocysteinase, glutathione-disulfide reductase
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1916 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 12.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD, 1mM NADH; Screen: JCSG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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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: Aug 19, 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: 1.73→30 Å / Num. obs: 188943 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.032 / Rsym value: 0.059 / Χ2: 1.002 / Net I/σ(I): 22.1
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2 / Num. unique obs: 9415 / CC1/2: 0.739 / Rpim(I) all: 0.4 / Rsym value: 0.722 / Χ2: 1.029 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V36

5v36


Resolution: 1.73→29.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.242 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19478 9443 5 %RANDOM
Rwork0.1624 ---
obs0.164 178985 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å2-0.43 Å2
2---0.66 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.73→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13890 0 243 1916 16049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213598
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9720336
X-RAY DIFFRACTIONr_angle_other_deg0.873331649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.01151911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85724.841690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.533152538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.61574
X-RAY DIFFRACTIONr_chiral_restr0.0860.22196
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0217063
X-RAY DIFFRACTIONr_gen_planes_other0.0190.023023
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_it0.7571.4367486
X-RAY DIFFRACTIONr_mcbond_other0.7571.4357485
X-RAY DIFFRACTIONr_mcangle_it1.2592.1489448
X-RAY DIFFRACTIONr_mcangle_other1.2592.1489449
X-RAY DIFFRACTIONr_scbond_it1.2141.6597476
X-RAY DIFFRACTIONr_scbond_other1.2141.6597477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9392.41810888
X-RAY DIFFRACTIONr_long_range_B_refined5.49619.17517772
X-RAY DIFFRACTIONr_long_range_B_other5.24417.93717204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 704 -
Rwork0.265 13188 -
obs--99.99 %
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)
11.45840.8188-0.42250.6871-0.27860.2620.1334-0.103-0.05150.1051-0.0810.07860.06730.0079-0.05240.1503-0.0453-0.01140.02710.00430.1338-20.721273.1687102.6852
21.23360.2140.11490.6186-0.02660.20410.1437-0.1188-0.14660.1503-0.09340.01550.1095-0.0073-0.05030.188-0.0517-0.03640.02780.02610.1267-15.880266.3686108.2108
31.50060.54281.04011.297-0.14382.64330.277-0.0118-0.29180.0481-0.0831-0.21370.37140.1728-0.19390.2020.0353-0.08860.02120.00220.27081.416356.5323102.2695
41.50850.4864-0.33740.8948-0.07620.42780.11430.0619-0.17860.039-0.02850.08950.1317-0.0467-0.08580.1855-0.0436-0.05950.02290.00780.1897-28.884159.573396.3944
53.67633.51741.51416.18141.76921.68580.01240.1361-0.4176-0.16830.1027-0.32610.20280.0517-0.11510.15060.0522-0.02620.047-0.06070.1157-5.330962.007277.6078
60.82760.04320.2251.6971-0.37980.82850.01380.1076-0.1315-0.24550.0611-0.02340.1954-0.0369-0.07490.16670.0015-0.01940.0392-0.04890.112-11.571968.592975.7661
70.3409-0.01130.23740.34340.07552.17980.05220.1006-0.0177-0.0880.0142-0.09070.11010.1951-0.06640.10770.01810.01110.0409-0.02620.09664.891485.49767.0049
80.4781-0.28160.26671.2872-0.33860.9721-0.04870.01180.0436-0.02540.0437-0.0587-0.1603-0.02630.0050.1370.0215-0.01530.0389-0.02650.0827-1.579103.271678.8013
91.12760.8128-0.11952.4195-0.45141.0739-0.02350.0220.04580.17770.04720.0306-0.1973-0.1346-0.02380.16720.0663-0.01690.0358-0.01810.0693-7.3054106.832182.0607
100.5518-0.1016-0.24230.3923-0.27871.71780.01270.08170.0197-0.10930.01540.05880.0277-0.1872-0.02820.13230.0007-0.0230.0491-0.02320.0861-10.813587.434559.3503
115.062-0.13755.19411.0911-0.22896.0948-0.0991-0.24620.1110.0619-0.02070.1744-0.1617-0.4520.11980.01230.0210.01950.0693-0.00130.0976-24.83687.462586.3464
121.07290.1840.46961.4141-0.22981.52110.0368-0.0073-0.0689-0.00920.07690.16970.0996-0.2594-0.11370.0895-0.0016-0.00840.08060.00570.1158-23.266879.499782.4363
130.5447-0.3110.92190.7048-0.7891.75120.01220.14350.0182-0.2304-0.1667-0.10410.18560.29640.15450.20450.07360.08860.11550.03860.125213.655139.94143.8713
142.0962-0.25771.03761.4077-0.68772.1309-0.07570.23350.2388-0.2845-0.218-0.2747-0.11420.37860.29370.1890.01940.09610.07940.08070.119613.3550.52739.5505
151.3752-1.45020.32562.4829-0.80682.3534-0.07130.27610.5462-0.1534-0.4335-1.0347-0.44150.91620.50490.2231-0.18090.05220.37710.25660.626128.601358.529247.4612
160.5272-0.02730.58291.4292-0.63972.0121-0.0863-0.08770.10510.0161-0.0131-0.0457-0.3148-0.15010.09930.17930.07170.00180.0362-0.01820.0766-0.137554.83450.1358
175.0095-4.9204-2.16897.03351.31321.6305-0.1542-0.20720.42860.11460.0899-0.5293-0.21840.28290.06430.2696-0.0592-0.18830.1661-0.00220.267521.123552.248471.9181
181.3334-1.01470.41141.6101-0.88211.3319-0.2569-0.02870.28070.32260.0175-0.3054-0.31620.04170.23940.17480.0348-0.07550.0302-0.01870.148514.148946.141972.4437
190.1417-0.21950.09710.3982-0.24752.18030.03420.10560.0897-0.0435-0.1537-0.195-0.03810.31180.11950.08230.02270.02210.11390.05130.165926.597630.417680.1731
200.2814-0.25930.09270.7314-0.02381.63810.03580.04040.05960.0253-0.1366-0.1944-0.10320.29160.10080.07190.00050.00410.09890.04580.193530.432428.068788.5294
210.43720.263-0.31862.1598-0.90991.36760.02680.0946-0.1308-0.2465-0.2115-0.32690.32110.19730.18470.19480.11280.08620.1052-0.00240.173224.309511.322971.4054
221.7234-1.16850.04423.2188-1.3441.86490.05340.141-0.1267-0.4992-0.1733-0.18470.48130.11770.11990.26560.07280.08750.0762-0.04870.131119.1197.828967.4577
230.3113-0.08070.41290.4285-0.48361.3193-0.00680.01590.0279-0.0292-0.0371-0.03290.04-0.12150.04380.11280.0270.01440.0886-0.01480.15299.711227.383282.2782
240.7786-0.17080.10561.717-0.70211.5936-0.03830.05780.0839-0.05950.06620.041-0.0153-0.0822-0.02780.11220.0380.00920.0723-0.00580.08213.67335.291663.9202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 74
2X-RAY DIFFRACTION2A75 - 200
3X-RAY DIFFRACTION3A201 - 258
4X-RAY DIFFRACTION4A259 - 352
5X-RAY DIFFRACTION5A353 - 384
6X-RAY DIFFRACTION6A385 - 449
7X-RAY DIFFRACTION7B2 - 142
8X-RAY DIFFRACTION8B143 - 200
9X-RAY DIFFRACTION9B201 - 260
10X-RAY DIFFRACTION10B261 - 357
11X-RAY DIFFRACTION11B358 - 384
12X-RAY DIFFRACTION12B385 - 449
13X-RAY DIFFRACTION13C1 - 89
14X-RAY DIFFRACTION14C90 - 200
15X-RAY DIFFRACTION15C201 - 267
16X-RAY DIFFRACTION16C268 - 354
17X-RAY DIFFRACTION17C355 - 384
18X-RAY DIFFRACTION18C385 - 449
19X-RAY DIFFRACTION19D0 - 74
20X-RAY DIFFRACTION20D75 - 142
21X-RAY DIFFRACTION21D143 - 200
22X-RAY DIFFRACTION22D201 - 261
23X-RAY DIFFRACTION23D262 - 384
24X-RAY DIFFRACTION24D385 - 449

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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