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- PDB-1mli: CRYSTAL STRUCTURE OF MUCONOLACTONE ISOMERASE AT 3.3 ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 1mli
TitleCRYSTAL STRUCTURE OF MUCONOLACTONE ISOMERASE AT 3.3 ANGSTROMS RESOLUTION
ComponentsMUCONOLACTONE ISOMERASE
KeywordsINTRAMOLECULAR OXIDOREDUCTASE
Function / homologymuconolactone Delta-isomerase / muconolactone delta-isomerase activity / Muconolactone delta-isomerase / Muconolactone isomerase domain / Muconolactone delta-isomerase / beta-ketoadipate pathway / Dimeric alpha-beta barrel / Muconolactone Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsKatti, S.K. / Katz, B.A. / Wyckoff, H.W.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Crystal structure of muconolactone isomerase at 3.3 A resolution.
Authors: Katti, S.K. / Katz, B.A. / Wyckoff, H.W.
#1: Journal: J.Mol.Biol. / Year: 1985
Title: Low Resolution Crystal Structure of Muconolactone Isomerase. A Decamer with a 5-Fold Symmetry Axis
Authors: Katz, B.A. / Ollis, D. / Wyckoff, H.W.
History
DepositionNov 2, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MUCONOLACTONE ISOMERASE
B: MUCONOLACTONE ISOMERASE
C: MUCONOLACTONE ISOMERASE
D: MUCONOLACTONE ISOMERASE
E: MUCONOLACTONE ISOMERASE
F: MUCONOLACTONE ISOMERASE
G: MUCONOLACTONE ISOMERASE
H: MUCONOLACTONE ISOMERASE
I: MUCONOLACTONE ISOMERASE
J: MUCONOLACTONE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)111,75810
Polymers111,75810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.840, 105.630, 77.210
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999951, -0.007558, -0.006425), (-0.007558, 0.160956, 0.986933), (-0.006425, 0.986933, -0.161005)32.628, -18.352, 21.838
2given(0.99998, -0.002699, 0.005641), (0.006199, 0.30903, -0.951032), (0.000823, 0.951049, 0.30904)-0.107, 18.74, 12.67
DetailsMUCONOLACTONE ISOMERASE IS A DECAMER WITH A CLOSED 52 POINT NONCRYSTALLOGRAPHIC SYMMETRY. THE FIVE-FOLD AXIS IS ALMOST ALONG THE A-AXIS. THE TWO-FOLD AXES ARE IN A PLANE PERPENDICULAR TO THE FIVE-FOLD DIRECTION. THE MOLECULAR CENTER IS AT (16.250, 0.692, 19.308). THE TWO-FOLD SYMMETRY OPERATOR IS PRESENTED ON *MTRIX 1* RECORDS BELOW AND THE FIVE-FOLD SYMMETRY OPERATOR IS PRESENTED ON *MTRIX 2* RECORDS BELOW. THE FOLLOWING PROCEDURE CAN BE USED TO GENERATE COORDINATES OF A DECAMER FROM THE MONOMER COORDINATES PRESENTED IN THIS ENTRY. 1. APPLY THE TRANSFORMATION PRESENTED ON THE *MTRIX 1* RECORDS BELOW TO THE MONOMER IN THIS ENTRY TO GENERATE A TWO-FOLD RELATED MONOMER. 2. APPLY THE TRANSFORMATION PRESENTED ON THE *MTRIX 2* RECORDS BELOW TO THE DIMER GENERATED IN STEP 1 TO GENERATE A FIVE-FOLD RELATED DIMER. 3. PERFORM STEP 2 THREE MORE TIMES, EACH TIME APPLYING THE TRANSFORMATION TO THE NEWLY-GENERATED DIMER. THIS WILL YIELD A TOTAL OF FIVE DIMERS (TEN MONOMERS).

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Components

#1: Protein
MUCONOLACTONE ISOMERASE / Coordinate model: Cα atoms only


Mass: 11175.833 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P00948, muconolactone Delta-isomerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %satammonium sulfate1drop
38 %satsodium sulfate1reservoir
2MES1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.3 Å / Num. obs: 14090 / Rmerge(I) obs: 0.082

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Processing

RefinementHighest resolution: 3.3 Å
Refinement stepCycle: LAST / Highest resolution: 3.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 0 0 960
Refinement
*PLUS
Num. reflection all: 9329 / Num. reflection obs: 14027 / Rfactor obs: 0.39
Solvent computation
*PLUS
Displacement parameters
*PLUS

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