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

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Basic information

Entry
Database: PDB / ID: 3hds
TitleCrystal structure of 4-methylmuconolactone methylisomerase in complex with MES
Components
  • 4-methylmuconolactone methylisomerase
  • short peptide ASWSA
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
4-carboxymethyl-4-methylbutenolide mutase
Similarity search - Component
Biological speciesPseudomonas reinekei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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 7, 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
E: short peptide ASWSA
F: short peptide ASWSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,39710
Polymers55,6166
Non-polymers7814
Water7,584421
1
A: 4-methylmuconolactone methylisomerase
D: 4-methylmuconolactone methylisomerase
E: short peptide ASWSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1985
Polymers27,8083
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-20 kcal/mol
Surface area10930 Å2
MethodPISA
2
B: 4-methylmuconolactone methylisomerase
C: 4-methylmuconolactone methylisomerase
F: short peptide ASWSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1985
Polymers27,8083
Non-polymers3902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-20 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.872, 84.160, 150.160
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: Protein/peptide short peptide ASWSA


Mass: 520.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionNumber: 733384 / Rmerge(I) obs: 0.084 / D res high: 1.45 Å / Num. obs: 91817 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1042.0731696.610.059
610109199.910.059
46320510010.047
34609510010.05
2.73390510010.06
2.52.7371610010.067
2.42.5232710010.074
2.32.4278810010.078
2.22.3326510010.081
2.12.2391410010.086
22.1477010010.096
1.92579910010.121
1.81.9716710010.158
1.71.8892010010.227
1.61.71125610010.326
1.51.61447510010.459
1.451.5880810010.716
ReflectionResolution: 1.45→42.07 Å / Num. obs: 91817 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.99 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.46
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.50.7162.81100
1.5-1.60.4594.41100
1.6-1.70.3266.21100
1.7-1.80.2278.71100
1.8-1.90.158121100
1.9-20.12115.11100
2-2.10.09618.81100
2.1-2.20.08620.51100
2.2-2.30.08121.91100
2.3-2.40.078231100
2.4-2.50.07424.31100
2.5-2.70.06725.81100
2.7-30.0627.91100
3-40.0532.21100
4-60.04734.31100
6-100.05933.7199.9
10-42.070.05930.7196.6

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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 2IFX

2ifx


Resolution: 1.45→42.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.156 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20912 4590 5 %RANDOM
Rwork0.18482 ---
obs0.18602 87224 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.936 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 48 421 4250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9585832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77623.271214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56415759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5671530
X-RAY DIFFRACTIONr_chiral_restr0.110.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213324
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_it1.0371.52477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81124046
X-RAY DIFFRACTIONr_scbond_it2.55131808
X-RAY DIFFRACTIONr_scangle_it4.1134.51774
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 336 -
Rwork0.237 6385 -
obs--100 %

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