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- PDB-4fpi: Crystal Structure of 5-chloromuconolactone isomerase from Rhodoco... -

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Basic information

Entry
Database: PDB / ID: 4fpi
TitleCrystal Structure of 5-chloromuconolactone isomerase from Rhodococcus opacus 1CP
Components5-chloromuconolactone dehalogenase
KeywordsISOMERASE / intramolecular oxidoreductase
Function / homology
Function and homology information


muconolactone Delta-isomerase / muconolactone delta-isomerase activity / beta-ketoadipate pathway
Similarity search - Function
Muconolactone delta-isomerase / Muconolactone isomerase domain / Muconolactone delta-isomerase / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Muconolactone Delta-isomerase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFerraroni, M. / Kolomytseva, M. / Briganti, F. / Golovleva, L.A. / Scozzafava, A.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: X-ray crystallographic and molecular docking studies on a unique chloromuconolactone dehalogenase from Rhodococcus opacus 1CP.
Authors: Ferraroni, M. / Kolomytseva, M. / Golovleva, L.A. / Scozzafava, A.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-chloromuconolactone dehalogenase
B: 5-chloromuconolactone dehalogenase
C: 5-chloromuconolactone dehalogenase
D: 5-chloromuconolactone dehalogenase
E: 5-chloromuconolactone dehalogenase
F: 5-chloromuconolactone dehalogenase
G: 5-chloromuconolactone dehalogenase
H: 5-chloromuconolactone dehalogenase
I: 5-chloromuconolactone dehalogenase
J: 5-chloromuconolactone dehalogenase
K: 5-chloromuconolactone dehalogenase
L: 5-chloromuconolactone dehalogenase
M: 5-chloromuconolactone dehalogenase
N: 5-chloromuconolactone dehalogenase
O: 5-chloromuconolactone dehalogenase
P: 5-chloromuconolactone dehalogenase
R: 5-chloromuconolactone dehalogenase
S: 5-chloromuconolactone dehalogenase
T: 5-chloromuconolactone dehalogenase
U: 5-chloromuconolactone dehalogenase


Theoretical massNumber of molelcules
Total (without water)224,01420
Polymers224,01420
Non-polymers00
Water11,061614
1
A: 5-chloromuconolactone dehalogenase
B: 5-chloromuconolactone dehalogenase
C: 5-chloromuconolactone dehalogenase
D: 5-chloromuconolactone dehalogenase
E: 5-chloromuconolactone dehalogenase
F: 5-chloromuconolactone dehalogenase
G: 5-chloromuconolactone dehalogenase
H: 5-chloromuconolactone dehalogenase
I: 5-chloromuconolactone dehalogenase
J: 5-chloromuconolactone dehalogenase


Theoretical massNumber of molelcules
Total (without water)112,00710
Polymers112,00710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24050 Å2
ΔGint-97 kcal/mol
Surface area41250 Å2
MethodPISA
2
K: 5-chloromuconolactone dehalogenase
L: 5-chloromuconolactone dehalogenase
M: 5-chloromuconolactone dehalogenase
N: 5-chloromuconolactone dehalogenase
O: 5-chloromuconolactone dehalogenase
P: 5-chloromuconolactone dehalogenase
R: 5-chloromuconolactone dehalogenase
S: 5-chloromuconolactone dehalogenase
T: 5-chloromuconolactone dehalogenase
U: 5-chloromuconolactone dehalogenase


Theoretical massNumber of molelcules
Total (without water)112,00710
Polymers112,00710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23770 Å2
ΔGint-94 kcal/mol
Surface area41670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.187, 79.657, 125.907
Angle α, β, γ (deg.)90.000, 105.540, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a decamer. There are 2 biological units in the asymmetric unit

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Components

#1: Protein
5-chloromuconolactone dehalogenase


Mass: 11200.680 Da / Num. of mol.: 20 / Mutation: P17S / Source method: isolated from a natural source / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP / References: UniProt: Q8G9L0, muconolactone Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE PROTEIN IS NOT A MUTANT. P17S IS NOT A MUTATION BUT IT IS A CORRECTION THAT ...AUTHORS STATE THAT THE PROTEIN IS NOT A MUTANT. P17S IS NOT A MUTATION BUT IT IS A CORRECTION THAT WE MADE TO THE SEQUENCE BASED ON THE CRYSTALLOGRAPHIC STRUCTURE FOR THE PROTEIN NATURALLY ISOLATED FROM BACTERIUM RHODOCOCCUS OPACUS 1CP

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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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: PEG8000, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→121.302 Å / Num. all: 133960 / Num. obs: 133960 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.213.30.5611.461208186620.56194.2
2.21-2.353.30.4291.659392180730.42996.6
2.35-2.513.30.3022.357640174010.30298.9
2.51-2.713.30.2013.854805163820.20199.9
2.71-2.973.40.1395.550747151030.139100
2.97-3.323.40.0818.946266137450.081100
3.32-3.833.40.0649.540714120840.064100
3.83-4.73.40.05610.634460102360.05699.8
4.7-6.643.40.0414.72666979200.0499.5
6.64-66.5193.30.03215.21442943540.03297.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å29.81 Å
Translation3.5 Å29.81 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2952 / WRfactor Rwork: 0.2254 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.771 / SU B: 8.518 / SU ML: 0.219 / SU R Cruickshank DPI: 0.2961 / SU Rfree: 0.2554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3008 5903 5 %RANDOM
Rwork0.2281 ---
obs0.2317 117344 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.44 Å2 / Biso mean: 49.3208 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-2.33 Å2
2--1.13 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15290 0 0 614 15904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02115750
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.94421420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35751865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72322.725778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94152588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5315143
X-RAY DIFFRACTIONr_chiral_restr0.1050.22306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112123
X-RAY DIFFRACTIONr_mcbond_it0.81.59398
X-RAY DIFFRACTIONr_mcangle_it1.469215152
X-RAY DIFFRACTIONr_scbond_it2.09336352
X-RAY DIFFRACTIONr_scangle_it3.2644.56264
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 428 -
Rwork0.29 7881 -
all-8309 -
obs--95.47 %

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