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- PDB-3hf5: Crystal structure of 4-methylmuconolactone methylisomerase in com... -

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Basic information

Entry
Database: PDB / ID: 3hf5
TitleCrystal structure of 4-methylmuconolactone methylisomerase in complex with 3-methylmuconolactone
Components4-methylmuconolactone methylisomerase
KeywordsISOMERASE / ferredoxin / ferredoxin-like fold / beta-barrel / 4-methylmuconolactone methylisomerase / biodegradation / ortho-cleavage
Function / homology
Function and homology information


4-carboxymethyl-4-methylbutenolide mutase / isomerase activity
Similarity search - Function
4-Methylmuconolactone methyl-isomerase / Methylmuconolactone methyl-isomerase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3ML / 4-carboxymethyl-4-methylbutenolide mutase
Similarity search - Component
Biological speciesPseudomonas reinekei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsMarin, M. / Heinz, D.W. / Pieper, D.H. / Klink, B.U.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure and catalytic mechanism of 4-methylmuconolactone methylisomerase
Authors: Marin, M. / Heinz, D.W. / Pieper, D.H. / Klink, B.U.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: 4-methylmuconolactone methylisomerase
B: 4-methylmuconolactone methylisomerase
C: 4-methylmuconolactone methylisomerase
D: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1998
Polymers54,5754
Non-polymers6254
Water9,836546
1
A: 4-methylmuconolactone methylisomerase
D: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6004
Polymers27,2872
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-28 kcal/mol
Surface area10960 Å2
MethodPISA
2
B: 4-methylmuconolactone methylisomerase
C: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6004
Polymers27,2872
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-27 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.760, 84.000, 150.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
4-methylmuconolactone methylisomerase


Mass: 13643.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas reinekei (bacteria) / Strain: MT1 / Gene: mmlI / Plasmid: pASKIBAmmlI / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: C5MR76, 4-carboxymethyl-4-methylbutenolide mutase
#2: Chemical
ChemComp-3ML / [(2S)-3-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid / 3-methylmuconolactone


Mass: 156.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 5
Details: 25% PEG 1500, 0.1M MMT, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.10505 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10505 Å / Relative weight: 1
ReflectionNumber: 1003159 / Rmerge(I) obs: 0.089 / D res high: 1.4 Å / D res low: 42 Å / Num. obs: 101311 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
104229790.810.061
610108399.610.064
46317899.810.062
34607910010.065
2.73387410010.07
2.52.7370810010.072
2.42.5232310010.075
2.32.4276610010.077
2.22.3326410010.08
2.12.2390310010.082
22.1474510010.086
1.92577510010.097
1.81.9714210010.12
1.71.8887410010.162
1.61.71123010010.234
1.51.61436599.810.346
1.41.51870599.510.682
ReflectionResolution: 1.4→42 Å / Num. obs: 101311 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.87
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.68 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefmac_5.5.0071refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HDS

3hds


Resolution: 1.4→40.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.975 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 5065 5 %RANDOM
Rwork0.17744 ---
obs0.17895 96243 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 44 546 4308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9665984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36423.364217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43815802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9691531
X-RAY DIFFRACTIONr_chiral_restr0.1260.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213485
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2091.52536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05224177
X-RAY DIFFRACTIONr_scbond_it2.79131843
X-RAY DIFFRACTIONr_scangle_it4.4074.51792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 370 -
Rwork0.237 7020 -
obs--99.43 %

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