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- PDB-3lxz: Structure of probable Glutathione S-transferase(PP0183) from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3lxz
TitleStructure of probable Glutathione S-transferase(PP0183) from Pseudomonas putida
ComponentsGlutathione S-transferase family protein
KeywordsTRANSFERASE / structural genomics / Glutathione S-transferase / PP0183 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
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 S-transferase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of probable Glutathione S-transferase(PP0183) from Pseudomonas putida
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase family protein
B: Glutathione S-transferase family protein
C: Glutathione S-transferase family protein
D: Glutathione S-transferase family protein


Theoretical massNumber of molelcules
Total (without water)103,9554
Polymers103,9554
Non-polymers00
Water11,764653
1
A: Glutathione S-transferase family protein

B: Glutathione S-transferase family protein


Theoretical massNumber of molelcules
Total (without water)51,9772
Polymers51,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3300 Å2
ΔGint-18 kcal/mol
Surface area18840 Å2
MethodPISA
2
C: Glutathione S-transferase family protein
D: Glutathione S-transferase family protein


Theoretical massNumber of molelcules
Total (without water)51,9772
Polymers51,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-16 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.047, 66.358, 88.659
Angle α, β, γ (deg.)89.960, 85.270, 87.040
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutathione S-transferase family protein


Mass: 25988.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP0183 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88RE7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M Ammonium(di-) Tartrate pH 7, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 98088 / % possible obs: 91.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Χ2: 1.856 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.76-1.7930.42650231.24593.7
1.79-1.823.10.38851061.29494.9
1.82-1.863.10.35550941.33994.8
1.86-1.93.10.47250931.72894.8
1.9-1.943.10.23550992.35695.1
1.94-1.983.10.26351081.55595
1.98-2.033.10.19250491.52395.3
2.03-2.093.10.15951541.66295.1
2.09-2.153.10.14351411.70895.5
2.15-2.2230.15344531.89482.8
2.22-2.32.20.12624782.23146.5
2.3-2.393.10.11352161.9496.4
2.39-2.53.10.10251651.8596.9
2.5-2.633.10.09652312.04197.5
2.63-2.793.10.09252432.18297.7
2.79-3.013.10.0852712.12698.2
3.01-3.313.20.07553162.08198.6
3.31-3.7930.06734312.00664
3.79-4.7830.06351622.01295.9
4.78-503.20.07152552.57198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXEmodel building
SHELXDphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.808 / SU B: 2.6 / SU ML: 0.082 / SU R Cruickshank DPI: 0.126 / SU Rfree: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4901 5 %RANDOM
Rwork0.196 ---
obs0.197 97747 90.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.05 Å2 / Biso mean: 21.555 Å2 / Biso min: 10.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å2-0.16 Å2-0.38 Å2
2---0.04 Å2-0.01 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6885 0 0 653 7538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227038
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9969525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3165895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59724.579297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.245151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9221533
X-RAY DIFFRACTIONr_chiral_restr0.1030.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215302
X-RAY DIFFRACTIONr_mcbond_it0.8311.54421
X-RAY DIFFRACTIONr_mcangle_it1.50227094
X-RAY DIFFRACTIONr_scbond_it2.58732617
X-RAY DIFFRACTIONr_scangle_it4.2534.52431
LS refinement shellResolution: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 337 -
Rwork0.236 6616 -
all-6953 -
obs--87.16 %

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