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- PDB-2ime: 2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathi... -

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Basic information

Entry
Database: PDB / ID: 2ime
Title2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathione-S-Transferase from Pseudomonas putida
Components2-hydroxychromene-2-carboxylate isomerase
KeywordsTRANSFERASE / isomerase / glutathione / kgst / kappa gst
Function / homology
Function and homology information


2-hydroxychromene-2-carboxylate isomerase / 2-hydroxychromene-2-carboxylate isomerase activity / naphthalene catabolic process / glutathione peroxidase activity / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
2-hydroxychromene-2-carboxylate isomerase NahD-like / HCCA isomerase/glutathione S-transferase kappa / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-HYDROXY-2H-CHROMENE-2-CARBOXYLIC ACID / GLUTATHIONE / PHOSPHATE ION / (3E)-4-(2-HYDROXYPHENYL)-2-OXOBUT-3-ENOIC ACID / 2-hydroxychromene-2-carboxylate isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsThompson, L.C. / Ladner, J.E. / Codreanu, S.G. / Harp, J. / Gilliland, G.L. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2007
Title: 2-Hydroxychromene-2-carboxylic Acid Isomerase: A Kappa Class Glutathione Transferase from Pseudomonas putida
Authors: Thompson, L.C. / Ladner, J.E. / Codreanu, S.G. / Harp, J. / Gilliland, G.L. / Armstrong, R.N.
History
DepositionOct 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 2-hydroxychromene-2-carboxylate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2818
Polymers23,0831
Non-polymers1,1987
Water2,900161
1
A: 2-hydroxychromene-2-carboxylate isomerase
hetero molecules

A: 2-hydroxychromene-2-carboxylate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,56216
Polymers46,1662
Non-polymers2,39614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7470 Å2
ΔGint-27 kcal/mol
Surface area18000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.126, 75.833, 38.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

DetailsThe second part of the biological dimer is generated by -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-hydroxychromene-2-carboxylate isomerase / HCCA isomerase


Mass: 23083.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: nahD / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51948, glutathione transferase

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Non-polymers , 6 types, 168 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-TOH / (3E)-4-(2-HYDROXYPHENYL)-2-OXOBUT-3-ENOIC ACID


Mass: 192.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O4
#5: Chemical ChemComp-2C2 / (2S)-2-HYDROXY-2H-CHROMENE-2-CARBOXYLIC ACID


Mass: 192.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O4
#6: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 294 K / Method: microbatch under oil / pH: 6.1
Details: crystallization solution: 1.2M sodium dihydrogen phosphate, 0.8M potassium hydrogen phosphate,0.2M lithium sulfate, 0.1M CAPS pH 6.1. Protein and crystallization solutions were mixed 1:1., ...Details: crystallization solution: 1.2M sodium dihydrogen phosphate, 0.8M potassium hydrogen phosphate,0.2M lithium sulfate, 0.1M CAPS pH 6.1. Protein and crystallization solutions were mixed 1:1., microbatch under oil, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→18.14 Å / Num. all: 23427 / Num. obs: 23427 / % possible obs: 100 % / Redundancy: 18.14 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 17.47 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 8.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→18.14 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.358 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23518 1204 5.1 %RANDOM
Rwork0.18606 ---
obs0.18859 22223 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2---0.76 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 77 161 1868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.9932485
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0955202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95923.19194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2121517
X-RAY DIFFRACTIONr_chiral_restr0.2320.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2927
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21261
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.361.51061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98121665
X-RAY DIFFRACTIONr_scbond_it2.9713896
X-RAY DIFFRACTIONr_scangle_it4.2024.5820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.791 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 188 -
Rwork0.263 3155 -
obs--99.85 %

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