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- PDB-3m8n: Crystal structure of a possible gutathione S-tranferase from Rhod... -

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Basic information

Entry
Database: PDB / ID: 3m8n
TitleCrystal structure of a possible gutathione S-tranferase from Rhodopseudomonas palustris
ComponentsPossible glutathione S-transferase
KeywordsTRANSFERASE / PSI-II / Structural Genomics / Protein Structure Initiative / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
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 / 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
Possible glutathione S-transferase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a possible gutathione S-tranferase from Rhodopseudomonas palustris
Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Possible glutathione S-transferase
B: Possible glutathione S-transferase
C: Possible glutathione S-transferase
D: Possible glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0767
Polymers102,7884
Non-polymers2883
Water4,306239
1
A: Possible glutathione S-transferase
B: Possible glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5864
Polymers51,3942
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-40 kcal/mol
Surface area17220 Å2
MethodPISA
2
C: Possible glutathione S-transferase
D: Possible glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4903
Polymers51,3942
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-29 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.972, 105.088, 152.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Possible glutathione S-transferase


Mass: 25696.986 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: gstA1, RPA4332 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N1S2, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 2.0M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→45.7 Å / Num. all: 53934 / Num. obs: 53728 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.5 / % possible all: 75.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SOLVE& Resolvephasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→45.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.022 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25935 1718 3.2 %RANDOM
Rwork0.19884 ---
obs0.2014 52010 91.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.04→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 15 239 6636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226569
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9488960
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39623.386316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3571546
X-RAY DIFFRACTIONr_chiral_restr0.1390.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215097
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0191.54000
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92526390
X-RAY DIFFRACTIONr_scbond_it3.06232569
X-RAY DIFFRACTIONr_scangle_it4.6694.52570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.326 3125 -
Rfree-0 -
obs--72.96 %

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