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- PDB-2jl4: Holo structure of Maleyl Pyruvate Isomerase, a bacterial glutathi... -

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Basic information

Entry
Database: PDB / ID: 2jl4
TitleHolo structure of Maleyl Pyruvate Isomerase, a bacterial glutathione- s-transferase in Zeta class
ComponentsMALEYLPYRUVATE ISOMERASE
KeywordsISOMERASE / GLUTATHIONE-S-TRANSFERASE / GST / PLASMID / PYRUVATE / BACTERIAL / BIODEGRADATION / MALEYL PYRUVATE / FUMARYL PYRUVATE
Function / homology
Function and homology information


maleylpyruvate isomerase / maleylpyruvate isomerase activity / naphthalene catabolic process / maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / 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 Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / 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 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 / Maleylpyruvate isomerase
Similarity search - Component
Biological speciesRALSTONIA SP. U2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShoemark, D.K. / Y Zhou, N. / Williams, P.A. / Hadfield, A.T.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structure of Bacterial Glutathione-S-Transferase Maleyl Pyruvate Isomerase and Implications for Mechanism of Isomerisation.
Authors: Marsh, M. / Shoemark, D.K. / Jacob, A. / Robinson, C. / Cahill, B. / Zhou, N.Y. / Williams, P.A. / Hadfield, A.T.
#1: Journal: J.Bacteriol. / Year: 1998
Title: A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas Sp. Strain U2.
Authors: Fuenmayor, S.L. / Wild, M. / Boyes, A.L. / Williams, P.A.
History
DepositionSep 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALEYLPYRUVATE ISOMERASE
B: MALEYLPYRUVATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9374
Polymers47,3222
Non-polymers6152
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-33.7 kcal/mol
Surface area20120 Å2
MethodPQS
Unit cell
Length a, b, c (Å)60.332, 81.733, 88.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.0005, 0.00085), (-0.0005, 1, -0.00043), (-0.00085, -0.00043, -1)
Vector: -0.03232, 0.0089, 88.18721)

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Components

#1: Protein MALEYLPYRUVATE ISOMERASE / MALEYL PYRUVATE ISOMERASE


Mass: 23660.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SP. U2 (bacteria) / Description: VENEZUALAN OIL FIELDS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: O86043, maleylacetoacetate isomerase
#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.: 438 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL LYSINE VISIBLE WHICH COMES FROM HIS-TAG

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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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG 10K IN 0.1 M HEPES BUFFER AT PH 7.5, PROTEIN IN 20MM TRIS (PH 7.4), 2 MM GLUTATHIONE, 1 MM DTT AND 20 MM IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 19625 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.12
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.33 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FW1

1fw1


Resolution: 2.3→27.63 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.247 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 950 4.9 %RANDOM
Rwork0.211 ---
obs0.214 18582 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 40 438 3800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223480
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9774750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9295432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94422.927164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7951534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21822
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22367
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2403
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.23432194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06553434
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.12761465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.743101311
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 78
Rwork0.257 1322

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