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- PDB-4igj: Crystal structure of Maleylacetoacetate isomerase from Anaeromyxo... -

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Basic information

Entry
Database: PDB / ID: 4igj
TitleCrystal structure of Maleylacetoacetate isomerase from Anaeromyxobacter dehalogenans 2CP-1, target EFI-507175
ComponentsMaleylacetoacetate isomerase
KeywordsISOMERASE / Structural Genomics / Enzyme Function Initiative / glutathione
Function / homology
Function and homology information


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, 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 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, 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 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
Maleylacetoacetate isomerase
Similarity search - Component
Biological speciesAnaeromyxobacter dehalogenans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of Maleylacetoacetate isomerase from Anaeromyxobacter dehalogenans 2CP-1, target EFI-507175
Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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 / _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

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Assembly

Deposited unit
A: Maleylacetoacetate isomerase
B: Maleylacetoacetate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3694
Polymers55,1772
Non-polymers1922
Water5,585310
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-65 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.709, 80.817, 88.050
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 Maleylacetoacetate isomerase


Mass: 27588.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyxobacter dehalogenans (bacteria)
Strain: 2CP-1 / ATCC BAA-258 / Gene: A2cp1_3570 / Production host: Escherichia coli (E. coli) / References: UniProt: B8J605
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium citrate:HCl, pH 5.6, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.48→59.539 Å / Num. all: 76480 / Num. obs: 67101 / % possible obs: 87.7 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.3
Reflection shellResolution: 1.48→1.51 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JL4

2jl4


Resolution: 1.48→36.219 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 3339 4.98 %RANDOM
Rwork0.1857 ---
obs0.187 67030 87.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→36.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 10 310 3669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063547
X-RAY DIFFRACTIONf_angle_d1.0754848
X-RAY DIFFRACTIONf_dihedral_angle_d12.3351314
X-RAY DIFFRACTIONf_chiral_restr0.071513
X-RAY DIFFRACTIONf_plane_restr0.007645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50090.22841530.19962784X-RAY DIFFRACTION94
1.5009-1.52330.23761450.18852874X-RAY DIFFRACTION95
1.5233-1.54710.23011590.18412835X-RAY DIFFRACTION95
1.5471-1.57250.18991320.17892880X-RAY DIFFRACTION95
1.5725-1.59960.20061560.16852840X-RAY DIFFRACTION96
1.5996-1.62870.20861370.17232884X-RAY DIFFRACTION96
1.6287-1.660.1841470.17072867X-RAY DIFFRACTION96
1.66-1.69390.2081510.17382889X-RAY DIFFRACTION96
1.6939-1.73070.21291470.17492884X-RAY DIFFRACTION96
1.7307-1.7710.22111540.1772901X-RAY DIFFRACTION97
1.771-1.81530.18261470.1742898X-RAY DIFFRACTION97
1.8153-1.86440.21481650.18092907X-RAY DIFFRACTION97
1.8644-1.91920.2464640.20151273X-RAY DIFFRACTION84
1.9192-1.98120.2171150.20441941X-RAY DIFFRACTION77
1.9812-2.0520.23111410.19122955X-RAY DIFFRACTION97
2.052-2.13410.21831540.18092942X-RAY DIFFRACTION98
2.1341-2.23120.1881250.18062393X-RAY DIFFRACTION89
2.2312-2.34880.2337900.19311463X-RAY DIFFRACTION90
2.3488-2.4960.23151610.18382973X-RAY DIFFRACTION98
2.496-2.68860.19091410.193023X-RAY DIFFRACTION98
2.6886-2.95910.22641490.19123039X-RAY DIFFRACTION99
2.9591-3.3870.21181710.19243032X-RAY DIFFRACTION99
3.387-4.26620.1889580.16821080X-RAY DIFFRACTION35
4.2662-36.22940.20541770.1933134X-RAY DIFFRACTION97

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