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- PDB-1otg: 5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1otg
Title5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
Components5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
KeywordsISOMERASE / HYDROXYMUCONATE
Function / homology
Function and homology information


5-carboxymethyl-2-hydroxymuconate Delta-isomerase / 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / :
Similarity search - Function
5-carboxymethyl-2-hydroxymuconate isomerase / 5-carboxymethyl-2-hydroxymuconate isomerase / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-carboxymethyl-2-hydroxymuconate Delta-isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsSubramanya, H.S. / Roper, D.I. / Dauter, Z. / Dodson, E.J. / Davies, G.J. / Wilson, K.S. / Wigley, D.B.
CitationJournal: Biochemistry / Year: 1996
Title: Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases.
Authors: Subramanya, H.S. / Roper, D.I. / Dauter, Z. / Dodson, E.J. / Davies, G.J. / Wilson, K.S. / Wigley, D.B.
History
DepositionNov 9, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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: 5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
B: 5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
C: 5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,15910
Polymers42,4873
Non-polymers6727
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-169 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.300, 90.300, 129.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE


Mass: 14162.215 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C / Description: CHMI PROMOTER / Gene: CHM / Plasmid: PUC19 / Gene (production host): CHM / Production host: Escherichia coli (E. coli)
References: UniProt: Q05354, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1drop
21 %PEG2001drop
31 mMdithiothreitol1drop
43 Mammonium sulfate1drop
52.5-2.8 Mammonium sulfate1reservoir
610 mMTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 28779 / % possible obs: 89.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.049
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.1→10 Å /
RfactorNum. reflection
obs0.179 28526
Displacement parametersBiso mean: 32.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 35 201 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0510.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.911
X-RAY DIFFRACTIONp_mcangle_it1.632
X-RAY DIFFRACTIONp_scbond_it3.622.5
X-RAY DIFFRACTIONp_scangle_it5.645
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.1360.12
X-RAY DIFFRACTIONp_singtor_nbd0.2060.5
X-RAY DIFFRACTIONp_multtor_nbd0.2250.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.210.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.535
X-RAY DIFFRACTIONp_staggered_tor21.4615
X-RAY DIFFRACTIONp_orthonormal_tor22.9220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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