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- PDB-4w66: Crystal structure of Glutathione S-transferase domain protein fro... -

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Basic information

Entry
Database: PDB / ID: 4w66
TitleCrystal structure of Glutathione S-transferase domain protein from Haliangium ochraceum DSM 14365
ComponentsGlutathione S-transferase domain protein
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / GSH
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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 ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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 / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase domain protein
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.36 Å
AuthorsChang, C. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of Glutathione S-transferase domain protein from Haliangium ochraceum DSM 14365
Authors: Chang, C. / Chhor, G. / Clancy, S. / Joachimiak, A.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase domain protein
B: Glutathione S-transferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9394
Polymers54,3242
Non-polymers6152
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-24 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.400, 130.400, 70.147
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Detailsbiological unit is the same as asym.

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Components

#1: Protein Glutathione S-transferase domain protein


Mass: 27162.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (bacteria) / Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_6316 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D0LNW1
#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.: 130 / 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: 56.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Calcium Chloride, 0.1M This-Cl 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. all: 24264 / Num. obs: 24250 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.058 / Rrim(I) all: 0.133 / Χ2: 0.797 / Net I/av σ(I): 16.037 / Net I/σ(I): 7.3 / Num. measured all: 147328
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.36-2.45.30.98612120.7720.4670.908100
2.4-2.445.50.91511870.7790.4240.883100
2.44-2.495.70.84612090.8240.3830.8741000.93
2.49-2.545.90.71612220.8790.3190.8511000.785
2.54-2.66.10.65712040.8960.2880.8551000.718
2.6-2.666.20.63711900.8860.2780.8551000.696
2.66-2.726.20.54112000.930.2350.8451000.591
2.72-2.86.30.43412010.9470.1880.8251000.473
2.8-2.886.30.39212180.9420.1690.8111000.427
2.88-2.976.30.32712160.9520.1410.8051000.356
2.97-3.086.30.25712150.9680.110.7571000.28
3.08-3.26.30.1912040.9760.0820.7481000.207
3.2-3.356.30.13512010.9850.0580.7331000.147
3.35-3.536.20.11112230.9840.0480.7361000.121
3.53-3.756.20.09511990.9870.0411.0121000.104
3.75-4.036.20.07412110.9860.0320.8231000.081
4.03-4.446.20.0612310.9880.0260.761000.066
4.44-5.086.10.05112220.9910.0220.67399.90.056
5.08-6.460.04412330.9880.0190.51999.90.048
6.4-5060.04912520.9930.0210.7199.10.054

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Processing

Software
NameVersionClassification
HKL-3000data reduction
SBC-Collectdata collection
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
Cootmodel building
HKL-3000phasing
SCALEPACKdata scaling
RefinementResolution: 2.36→36.95 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.92 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.236
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1205 5.1 %RANDOM
Rwork0.1864 22422 --
obs0.189 22422 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.56 Å2 / Biso mean: 24.276 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 2.36→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 40 130 3751
Biso mean--78.88 31.98 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193704
X-RAY DIFFRACTIONr_bond_other_d0.0010.023583
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9825039
X-RAY DIFFRACTIONr_angle_other_deg0.76338166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14221.676173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09515553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2911546
X-RAY DIFFRACTIONr_chiral_restr0.0640.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02906
X-RAY DIFFRACTIONr_mcbond_it1.1752.2411821
X-RAY DIFFRACTIONr_mcbond_other1.1752.241820
X-RAY DIFFRACTIONr_mcangle_it2.0653.3522271
LS refinement shellResolution: 2.36→2.423 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 60 -
Rwork0.241 1229 -
all-1289 -
obs--72.82 %
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)
12.81720.5453-1.06422.1951-0.17934.7920.04550.08590.16570.126-0.0429-0.0204-0.12540.3357-0.00260.05170.0090.0070.04570.01110.052924.5671.298-6.296
28.4978-2.8509-0.84373.3863-4.3919.0908-0.0408-0.0910.19740.1622-0.0211-0.0978-0.29350.14870.06190.0288-0.031-0.03390.11440.02580.092238.82470.02-1.726
30.9383-0.1985-0.69791.9074-0.17622.0578-0.0364-0.07160.06160.0684-0.0310.0349-0.02470.10270.06740.04180.03840.00430.0556-0.00480.031620.57959.6830.032
410.7343-0.6784-3.42450.3806-0.06032.06160.0278-0.0625-0.1153-0.0677-0.10950.01610.2810.12650.08170.09910.0370.00960.0488-0.00650.008724.61546.123-15.125
57.29220.56292.01844.1084-2.77467.66740.1653-0.54120.06170.061-0.34160.377-0.0932-0.67630.17640.0501-0.00110.01030.1852-0.07130.12356.42859.917-4.766
65.05230.70370.99771.64362.33694.60590.05780.3039-0.0817-0.1936-0.0815-0.0484-0.2328-0.1260.02370.0639-0.0016-0.00380.0526-0.01150.031114.22154.119-18.98
76.2492-0.4703-1.24554.7952-0.72912.1120.1380.6007-0.0288-0.1802-0.08150.2446-0.1894-0.174-0.05640.05440.0111-0.01780.06450.00070.017515.1766.98-15.015
88.40747.4784.051512.41443.84865.56790.30480.78950.0426-0.07390.2738-0.2604-0.02050.3688-0.57860.1190.11250.0820.1480.05230.127928.08652.338-24.83
96.02410.36970.06242.9935-0.26913.8227-0.00920.2107-0.33380.10140.07780.05090.48620.1033-0.06860.2220.09840.04740.05610.01620.038721.83836.6539.248
102.329-0.5332-0.37411.7523-0.73081.31280.04930.0613-0.17540.1638-0.06140.00670.12080.1380.01210.11760.0702-0.00890.0668-0.00260.016522.46349.6976.737
110.64790.32650.80776.11015.652110.6669-0.06840.02330.105-0.2760.0778-0.3508-0.11741.1081-0.00940.04330.06180.00450.2570.02110.093540.2449.678-3.835
125.46571.45161.74389.13090.21827.1199-0.1072-0.94790.27240.7521-0.15270.1960.0730.13950.25990.19710.0747-0.04240.2155-0.03280.080230.10452.91319.053
135.8751-1.95820.20532.00910.57293.63650.03980.0285-0.1020.1149-0.1545-0.47240.34140.75550.11470.13840.1681-0.07360.34250.08170.25942.89246.2649.12
141.15720.35570.90085.8529-0.89784.439-0.0318-0.008-0.21320.63410.0963-0.76440.4150.8106-0.06440.2750.168-0.02340.2530.02250.193733.38438.70615.092
157.23077.09531.7958.80890.51824.5561-0.07790.09930.2238-0.1202-0.0498-0.1760.51790.61210.12770.26640.32040.0250.420.01490.272444.37637.976-3.988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 39
2X-RAY DIFFRACTION2A40 - 50
3X-RAY DIFFRACTION3A51 - 113
4X-RAY DIFFRACTION4A114 - 146
5X-RAY DIFFRACTION5A147 - 161
6X-RAY DIFFRACTION6A162 - 192
7X-RAY DIFFRACTION7A193 - 215
8X-RAY DIFFRACTION8A216 - 236
9X-RAY DIFFRACTION9B3 - 38
10X-RAY DIFFRACTION10B52 - 113
11X-RAY DIFFRACTION11B114 - 146
12X-RAY DIFFRACTION12B147 - 161
13X-RAY DIFFRACTION13B162 - 192
14X-RAY DIFFRACTION14B193 - 215
15X-RAY DIFFRACTION15B216 - 235

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