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- PDB-4hi7: Crystal structure of glutathione transferase homolog from drosoph... -

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Basic information

Entry
Database: PDB / ID: 4hi7
TitleCrystal structure of glutathione transferase homolog from drosophilia mojavensis, TARGET EFI-501819, with bound glutathione
ComponentsGI20122
KeywordsUNKNOWN FUNCTION / GST / glutathione S-transferase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Uncharacterized protein
Similarity search - Component
Biological speciesDrosophila mojavensis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutathione transferase homolog from drosophilia mojavensis, TARGET EFI-501819, with bound glutathione
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GI20122
B: GI20122
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7274
Polymers51,1132
Non-polymers6152
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-25 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.700, 50.700, 289.473
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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Components

#1: Protein GI20122 / GLUTATHIONE TRANSFERASE HOMOLOG


Mass: 25556.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila mojavensis (fry) / Gene: GI20122, Dmoj\GI20122, Dmoj_GI20122 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4KM86
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffution / pH: 6.5
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl), Reservoir (0.2 M NaCl, 0.1 M Tris-CL pH 6.5, 30% PEG3000), Cryoprotection (reservoir + 20% ethylene glycol), sitting drop vapor diffution, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 13, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.25→96.491 Å / Num. all: 116694 / Num. obs: 116694 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.25-1.323.50.4571.755616159790.45791.6
1.32-1.43.80.3482.260178156750.34894.5
1.4-1.494.10.259360351148570.25995.4
1.49-1.614.30.1794.260132140290.17996.6
1.61-1.774.50.1325.559030130620.13297.3
1.77-1.984.80.1026.756965119150.10297.7
1.98-2.2850.0837.753567106090.08397.8
2.28-2.85.60.0718.85117091050.07198.2
2.8-3.957.10.05311.35113672450.05399.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IL3

2il3


Resolution: 1.25→30.104 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8451 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 5870 5.04 %RANDOM
Rwork0.1999 ---
all0.2013 116521 --
obs0.2013 116521 95.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.01 Å2 / Biso mean: 14.1348 Å2 / Biso min: 2.45 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 40 670 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113651
X-RAY DIFFRACTIONf_angle_d1.4074968
X-RAY DIFFRACTIONf_chiral_restr0.09561
X-RAY DIFFRACTIONf_plane_restr0.008637
X-RAY DIFFRACTIONf_dihedral_angle_d15.3991380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.26420.33831960.31213403359989
1.2642-1.27910.3331870.3073382356991
1.2791-1.29470.30931900.30643514370492
1.2947-1.31110.31012000.28473500370093
1.3111-1.32830.28831780.2683555373393
1.3283-1.34650.27711820.25743527370994
1.3465-1.36570.25392350.25053565380095
1.3657-1.38610.26022120.25013553376595
1.3861-1.40780.28341850.25243664384995
1.4078-1.43090.28541840.2453543372795
1.4309-1.45550.25971750.24363659383495
1.4555-1.4820.2572070.23543609381696
1.482-1.51050.25811840.22593661384596
1.5105-1.54130.23622000.22053718391896
1.5413-1.57490.25721750.21823663383896
1.5749-1.61150.24851900.2093651384197
1.6115-1.65180.21051670.20853744391196
1.6518-1.69640.25272010.21173738393997
1.6964-1.74640.23241950.21123734392997
1.7464-1.80270.24941880.2183752394098
1.8027-1.86710.2442110.2043749396098
1.8671-1.94190.24491960.19793751394798
1.9419-2.03030.23061920.19513773396597
2.0303-2.13730.21632000.18813740394098
2.1373-2.27110.20211870.18293785397298
2.2711-2.44640.21122020.1823813401597
2.4464-2.69250.22791930.18363861405498
2.6925-3.08170.21592310.18143863409499
3.0817-3.88140.18842100.152140204230100
3.8814-30.1040.15952170.15454161437898
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)
10.5893-0.096-0.060.87510.23880.9136-0.02520.13260.1767-0.0852-0.00920.0091-0.11330.04430.01960.03840.0051-0.00920.05180.01640.046717.577621.85558.647
21.4780.82310.76861.45720.62421.7562-0.04580.01590.41510.0182-0.05830.0489-0.33050.13550.07130.1148-0.0259-0.00910.08080.01360.138720.204730.659413.241
30.89760.05950.09251.2468-0.22560.86820.01280.00520.0371-0.04570.03730.0832-0.013-0.0822-0.03590.02890.0152-0.00230.0550.00510.040510.598814.04517.5448
43.69492.4486-1.43392.3973-0.89892.02210.0531-0.09060.21850.0638-0.0329-0.1036-0.36740.2335-0.01560.0719-0.0126-0.00090.1124-0.00430.114834.584719.292618.2898
52.34111.56420.06041.6694-0.0540.6410.0055-0.1324-0.0243-0.0461-0.0605-0.01260.06520.20210.04120.04910.0203-0.0060.1133-0.00080.125935.22856.46519.1064
62.0982-1.4036-0.43034.6683-0.09573.37260.0869-0.0076-0.6554-0.00120.09660.29950.5434-0.1574-0.13470.10750.0002-0.03410.0731-0.01920.202615.6375-1.406812.1911
71.89590.6848-0.02540.6205-0.13350.5257-0.0184-0.0454-0.0737-0.0807-0.0006-0.0950.00580.15160.02160.03940.020.00060.0646-0.00120.04323.874610.573811.4771
80.6216-0.0036-0.05451.062-0.29770.29440.02750.1292-0.2826-0.14110.0229-0.14260.12630.2365-0.02520.09010.0504-0.00580.113-0.02940.103427.49312.6956.6101
90.44990.1130.19070.3486-0.14040.42810.03170.05590.0333-0.1494-0.1301-0.1027-0.0490.24030.0509-0.1022-0.0095-0.02290.20610.03780.096234.514617.14346.9911
100.9465-0.306-0.06930.89330.12850.92730.0845-0.1152-0.34050.0230.00440.11120.4692-0.1481-0.03260.1628-0.0428-0.03030.05660.03190.065915.22244.412639.4715
112.5528-0.605-0.20661.4514-0.00961.4410.1636-0.1353-0.19760.23520.0722-0.11960.7060.1616-0.1090.30670.0756-0.10440.16350.00290.133920.8792-0.552540.0576
123.4825-0.6094-0.91540.86970.69911.8286-0.0402-0.0002-0.4124-0.0660.02290.01250.33280.1322-0.0850.38660.2553-0.18670.0465-0.03590.218624.1911-4.69729.9669
131.28520.26980.26732.754-0.43831.17560.0479-0.026-0.22460.11890.06390.25140.2468-0.2746-0.0610.0952-0.0344-0.01740.0910.02140.05768.21586.79231.371
141.83220.15220.5710.65980.03091.03010.04110.00340.03360.02-0.0245-0.1645-0.02670.1663-0.01080.0418-0.01160.00060.0678-0.00030.06627.515918.998331.2282
151.3960.553-0.42361.25360.24611.13320.0281-0.1090.24670.025-0.0270.0593-0.2303-0.0494-0.010.07380.00990.00430.0597-0.01480.0617.79724.295639.632
165.26930.2782-0.32990.50810.04490.6503-0.0113-0.1784-0.00510.0827-0.0046-0.1613-0.1020.22950.00570.0814-0.0174-0.01070.14670.00510.078929.597213.557545.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 56 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 105 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 125 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 146 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 158 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 173 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 174 through 197 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 198 through 222 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 24 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 25 through 43 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 56 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 89 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 145 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 146 through 197 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 198 through 219 )B0

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