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- PDB-4lbp: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burk... -

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Basic information

Entry
Database: PDB / ID: 4lbp
Title5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burkholderia phenoliruptrix AC1100: Complex with 2,5-dihydroxybenzoquinone
Components5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
KeywordsLYASE
Function / homology
Function and homology information


: / YCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,5-dihydroxycyclohexa-2,5-diene-1,4-dione / YCII-related domain-containing protein
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHayes, R.P. / Lewis, K.M. / Xun, L. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Catalytic Mechanism of 5-Chlorohydroxyhydroquinone Dehydrochlorinase from the YCII Superfamily of Largely Unknown Function.
Authors: Hayes, R.P. / Lewis, K.M. / Xun, L. / Kang, C.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4622
Polymers11,3221
Non-polymers1401
Water1,40578
1
A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules

A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules

A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules

A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8508
Polymers45,2894
Non-polymers5604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation12_565x,x-y+1,-z1
Buried area8440 Å2
ΔGint-35 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.191, 90.191, 50.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-347-

HOH

31A-364-

HOH

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Components

#1: Protein 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)


Mass: 11322.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45075
#2: Chemical ChemComp-1WG / 2,5-dihydroxycyclohexa-2,5-diene-1,4-dione / 2,5-dihydroxybenzoquinone


Mass: 140.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 53.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (w/v) polyethylene glycol 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 10578 / Num. obs: 10578 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.87-1.91100
1.9-1.941100
1.94-1.971100
1.97-2.011100
2.01-2.061100
2.06-2.111100

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→45.096 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 1058 10.01 %
Rwork0.1887 --
obs0.1917 10571 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→45.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms772 0 10 78 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007813
X-RAY DIFFRACTIONf_angle_d1.0561100
X-RAY DIFFRACTIONf_dihedral_angle_d12.036293
X-RAY DIFFRACTIONf_chiral_restr0.079115
X-RAY DIFFRACTIONf_plane_restr0.004142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9540.24561300.1891167X-RAY DIFFRACTION100
1.954-2.0570.2331280.17661147X-RAY DIFFRACTION100
2.057-2.18590.24681270.19081154X-RAY DIFFRACTION100
2.1859-2.35470.1881320.19781175X-RAY DIFFRACTION100
2.3547-2.59160.23691300.19821177X-RAY DIFFRACTION100
2.5916-2.96660.22851320.19671186X-RAY DIFFRACTION100
2.9666-3.73730.22261340.19341203X-RAY DIFFRACTION100
3.7373-45.0960.2061450.1791304X-RAY DIFFRACTION100

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