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- PDB-4gci: Crystal structure of glutahtione s-transferase homolog from yersi... -

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Basic information

Entry
Database: PDB / ID: 4gci
TitleCrystal structure of glutahtione s-transferase homolog from yersinia pestis, target EFI-501894, with bound glutathione, monoclinic form
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / 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 S-transferase, N-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 domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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 / Glutathione S-transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 glutahtione s-transferase homolog from yersinia pestis, target EFI-501894, with bound glutathione, monoclinic form
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
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2335
Polymers47,5832
Non-polymers6503
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-31 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.741, 89.338, 57.546
Angle α, β, γ (deg.)90.000, 112.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase / Glutathionine S-transferase


Mass: 23791.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: gst, gst2, y1968, YP_2153 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8D0L3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 5.5
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.2 M Ammonium Acetate, 0.1 M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350); Cryoprotection (Reservoir, + 20% ethylene glycol), sitting drop ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.2 M Ammonium Acetate, 0.1 M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350); Cryoprotection (Reservoir, + 20% ethylene glycol), sitting drop vapor diffuction, 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 MX-225 / Detector: CCD / Date: Jul 20, 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: 1.5→53.257 Å / Num. all: 72798 / Num. obs: 72798 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.083 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.583.70.5771.339464106130.577100
1.58-1.683.70.41.937526100550.4100
1.68-1.793.80.2732.83538994320.273100
1.79-1.943.80.1714.33316187930.171100
1.94-2.123.80.11663066180920.116100
2.12-2.373.80.16.42786573160.1100
2.37-2.743.80.0916.82480965000.091100
2.74-3.353.80.0648.72091554620.064100
3.35-4.743.80.04612.31613942490.046100
4.74-22.8733.70.04113845822860.04196.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4G9H

4g9h


Resolution: 1.5→22.873 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8688 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 3669 5.04 %RANDOM
Rwork0.1756 ---
all0.1772 72757 --
obs0.1772 72757 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.25 Å2 / Biso mean: 32.2543 Å2 / Biso min: 17.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 41 511 3748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053359
X-RAY DIFFRACTIONf_angle_d1.0384566
X-RAY DIFFRACTIONf_chiral_restr0.064513
X-RAY DIFFRACTIONf_plane_restr0.005588
X-RAY DIFFRACTIONf_dihedral_angle_d13.8131268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51970.30871390.272127032842100
1.5197-1.54060.26231270.256326182745100
1.5406-1.56260.25121350.23926442779100
1.5626-1.58590.2891370.22226562793100
1.5859-1.61060.21481310.206826752806100
1.6106-1.6370.24551440.203226452789100
1.637-1.66530.21551360.196226222758100
1.6653-1.69550.23641430.196526952838100
1.6955-1.72810.22821360.201226342770100
1.7281-1.76340.2491410.193326502791100
1.7634-1.80170.23041530.18726832836100
1.8017-1.84360.20981410.17726022743100
1.8436-1.88970.19551320.173626762808100
1.8897-1.94080.23081330.171626672800100
1.9408-1.99790.19191400.175926512791100
1.9979-2.06230.20511340.1826692803100
2.0623-2.1360.18521470.17126602807100
2.136-2.22140.21641540.169826522806100
2.2214-2.32240.22371490.176326582807100
2.3224-2.44470.19791410.170726372778100
2.4447-2.59770.20951450.175426792824100
2.5977-2.79790.20391500.178726392789100
2.7979-3.07890.21111500.173326742824100
3.0789-3.5230.21851400.159926672807100
3.523-4.43340.17421390.148927042843100
4.4334-22.87550.18251520.16782628278097
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)
11.1849-0.2167-0.77641.4593-0.05651.7261-0.0103-0.1920.05280.30080.0554-0.0815-0.12420.0409-0.04790.24560.0022-0.03790.2268-0.01460.1723-4.378996.479974.272
21.7999-0.70250.03931.14390.31850.90150.10720.0949-0.203-0.1493-0.12360.3642-0.006-0.29310.02010.2132-0.0035-0.02040.2883-0.00980.3019-18.057684.401859.3598
30.9664-0.279-0.02491.50540.40771.1167-0.0006-0.082-0.10070.12310.0396-0.08480.08140.0609-0.04820.21860.0126-0.02050.20950.01360.2097-2.498982.090367.6262
42.3724-0.5786-0.42112.48020.50142.1436-0.0740.162-0.23710.13160.07370.33090.2416-0.0151-0.02840.2534-0.0110.0210.2290.01990.334-9.484474.66165.7684
53.6634-1.5153-0.59033.58740.63663.17470.088-0.3551-0.25060.51440.08220.10.3501-0.1679-0.16530.3987-0.0039-0.0420.31710.0580.2097-6.245383.366382.003
60.9492-0.0869-0.10121.6047-0.62422.04760.02270.0737-0.0258-0.1583-0.0235-0.12810.09570.0752-0.01650.2029-0.00150.01470.21-0.00970.23330.939197.593949.4698
72.09780.8436-0.43910.9951-0.43910.35620.01940.05610.05560.00910.02440.31150.0183-0.0993-0.0470.23330.02560.01530.28050.01750.3416-20.9979101.021256.3308
81.97220.388-0.62562.0358-0.7451.51560.06050.0250.36040.03240.06740.2356-0.1662-0.1402-0.1030.2040.01450.01530.20040.0110.2835-9.2429111.805151.3192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 105 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 141 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 168 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 188 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 201 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 105 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 141 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 142 through 201 )B0

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