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- PDB-4pqi: Crystal structure of glutathione transferase lambda3 from Populus... -

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Basic information

Entry
Database: PDB / ID: 4pqi
TitleCrystal structure of glutathione transferase lambda3 from Populus trichocarpa
ComponentsIn2-1 family protein, glutathione transferase lambda3
KeywordsTRANSFERASE / GST fold / Thiol-tansferase
Function / homology
Function and homology information


Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLallement, P.A. / Meux, E. / Gualberto, J.M. / Prosper, P. / Didierjean, C. / Haouz, A. / Saul, F. / Rouhier, N. / Hecker, A.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural and enzymatic insights into Lambda glutathione transferases from Populus trichocarpa, monomeric enzymes constituting an early divergent class specific to terrestrial plants.
Authors: Lallement, P.A. / Meux, E. / Gualberto, J.M. / Prosper, P. / Didierjean, C. / Saul, F. / Haouz, A. / Rouhier, N. / Hecker, A.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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: In2-1 family protein, glutathione transferase lambda3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9595
Polymers27,5321
Non-polymers4284
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.524, 77.013, 82.636
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 In2-1 family protein, glutathione transferase lambda3


Mass: 27531.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0006s13580g / Production host: Escherichia coli (E. coli) / References: UniProt: U5G7B9
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN SEQUENCE ARE DUE TO ALTERNATIVE SPLICING EVENTS ...AUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN SEQUENCE ARE DUE TO ALTERNATIVE SPLICING EVENTS (RESIDUES 2 TO 6) AND TO POLYMORPHISM (RESIDUES 156 AND 202)

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG4000, 200 mM calcium chloride and 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28255 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2012
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28255 Å / Relative weight: 1
ReflectionResolution: 1.95→38.51 Å / Num. all: 19546 / Num. obs: 19546 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.2
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Proxima1 SOLEILdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QAG

3qag


Resolution: 1.95→38.507 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1013 5.18 %RANDOM
Rwork0.1808 ---
obs0.183 19546 97.9 %-
all-19546 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 23 126 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082034
X-RAY DIFFRACTIONf_angle_d1.1082756
X-RAY DIFFRACTIONf_dihedral_angle_d13.661766
X-RAY DIFFRACTIONf_chiral_restr0.077295
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9502-2.0530.32341500.26612513X-RAY DIFFRACTION96
2.053-2.18160.30091470.24062602X-RAY DIFFRACTION98
2.1816-2.350.28161260.2112621X-RAY DIFFRACTION98
2.35-2.58650.23471440.20992639X-RAY DIFFRACTION98
2.5865-2.96060.25871220.20222668X-RAY DIFFRACTION98
2.9606-3.72960.24611580.17492669X-RAY DIFFRACTION98
3.7296-38.5140.17161660.14922819X-RAY DIFFRACTION99
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)
11.72990.56-0.12721.39280.31562.1786-0.13870.21810.4543-0.233-0.09760.5048-0.3281-0.40450.2260.31260.0412-0.09220.3220.00720.4194-24.8738-3.80862.0519
21.32370.77460.39852.31371.19631.9881-0.18240.06560.1058-0.23960.03810.1543-0.16690.12390.12220.30230.0081-0.04930.35130.01980.3048-17.3276-6.015.4612
35.19453.1706-1.02785.3422-0.5333.432-0.36070.22830.0228-0.14730.1885-0.47240.33811.06150.05190.41-0.0163-0.03620.62060.0210.3419-2.01122.965318.6871
42.49540.37560.93552.74270.7013.29890.0062-0.3298-0.00470.4612-0.24420.2001-0.16230.13790.21890.38140.00380.01640.3803-0.05850.3203-12.78631.606727.977
51.20460.35420.36072.264-0.35291.72660.0075-0.03740.32370.345-0.10880.7824-0.2219-0.42040.08930.38790.00520.06270.4057-0.08870.4982-20.99564.162926.3739
63.19281.6817-1.77663.5445-1.79464.7376-0.32610.04510.17250.06990.19861.04910.2294-0.91230.22980.4428-0.01380.03220.5551-0.15370.6998-29.1681-2.287619.8308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 217 )
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 240 )

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