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- PDB-3hfk: Crystal structure of 4-methylmuconolactone methylisomerase (H52A)... -

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Basic information

Entry
Database: PDB / ID: 3hfk
TitleCrystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with 4-methylmuconolactone
Components4-methylmuconolactone methylisomerase4-carboxymethyl-4-methylbutenolide mutase
KeywordsISOMERASE / ferredoxin / ferredoxin-like fold / beta-barrel / 4-methylmuconolactone methylisomerase / H52A / biodegradation / ortho-cleavage
Function / homology
Function and homology information


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-4ML / 4-methylmuconolactone methylisomerase
Similarity search - Component
Biological speciesPseudomonas reinekei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 12, 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)55,39911
Polymers54,3064
Non-polymers1,0937
Water9,332518
1
A: 4-methylmuconolactone methylisomerase
D: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6225
Polymers27,1532
Non-polymers4683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-26 kcal/mol
Surface area10850 Å2
MethodPISA
2
B: 4-methylmuconolactone methylisomerase
C: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7786
Polymers27,1532
Non-polymers6254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-26 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.170, 84.360, 150.470
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 / 4-carboxymethyl-4-methylbutenolide mutase


Mass: 13576.619 Da / Num. of mol.: 4 / Mutation: H52A
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, EC: 5.4.99.14
#2: Chemical
ChemComp-4ML / [(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid / 4-methylmuconolactone


Mass: 156.136 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H8O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
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: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionNumber: 298041 / Rmerge(I) obs: 0.113 / D res high: 1.9 Å / D res low: 75.24 Å / Num. obs: 41197 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1075.2432197.610.029
610110010010.037
46322510010.043
34611699.610.062
2.73391610010.099
2.42.7610310010.147
2.22.4592597.510.259
22.2874810010.327
1.9257439910.564
ReflectionResolution: 1.9→75.24 Å / Num. obs: 41197 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.23 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.71
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.15 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.5 / % possible all: 99

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Processing

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

3hds


Resolution: 1.9→40.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.38 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23131 2079 5 %RANDOM
Rwork0.18463 ---
obs0.18698 39116 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 77 518 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9715570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45323.269208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811532
X-RAY DIFFRACTIONr_chiral_restr0.1130.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213204
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_it0.9691.52338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68323813
X-RAY DIFFRACTIONr_scbond_it2.5831756
X-RAY DIFFRACTIONr_scangle_it4.0494.51737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 131 -
Rwork0.308 2760 -
obs--95.98 %

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