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

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Basic information

Entry
Database: PDB / ID: 4lbi
Title5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burkholderia phenoliruptrix AC1100: Selenomethionyl Apo-form
Components5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
KeywordsLYASE
Function / homology: / YCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / YCII-related domain-containing protein
Function and homology information
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.21 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 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
B: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
C: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
D: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)


Theoretical massNumber of molelcules
Total (without water)45,2894
Polymers45,2894
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-29 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.238, 158.010, 50.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-278-

HOH

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Components

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


Mass: 11322.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45075
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 2.29 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 16, 2011
RadiationMonochromator: Rigaku Varimax CrHR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.29 Å / Relative weight: 1
ReflectionResolution: 2.21→23.61 Å / Num. all: 21246 / Num. obs: 21246 / % possible obs: 77.3 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.21-2.29113.5
2.29-2.38135.3
2.38-2.49157
2.49-2.62187.6
2.62-2.79193.4
2.79-3194.3
3-3.3195.4
3.3-3.78196.5
3.78-4.75197.7
4.75-23.61198.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.21→23.607 Å / SU ML: 0.23 / σ(F): 1.48 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2000 9.42 %RANDOM
Rwork0.1704 ---
obs0.1738 21232 77.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→23.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 0 272 3220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073068
X-RAY DIFFRACTIONf_angle_d1.0464152
X-RAY DIFFRACTIONf_dihedral_angle_d12.3481116
X-RAY DIFFRACTIONf_chiral_restr0.069444
X-RAY DIFFRACTIONf_plane_restr0.004536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.26670.45200.3218195X-RAY DIFFRACTION11
2.2667-2.3280.3149470.2423448X-RAY DIFFRACTION26
2.328-2.39640.2422720.2046700X-RAY DIFFRACTION40
2.3964-2.47370.25021060.20291014X-RAY DIFFRACTION58
2.4737-2.5620.25561460.22291409X-RAY DIFFRACTION81
2.562-2.66440.29331710.22621646X-RAY DIFFRACTION93
2.6644-2.78550.23171710.20611640X-RAY DIFFRACTION94
2.7855-2.93210.24681730.20181659X-RAY DIFFRACTION94
2.9321-3.11550.22071750.20431685X-RAY DIFFRACTION95
3.1155-3.35540.23211780.18381713X-RAY DIFFRACTION96
3.3554-3.69190.21431790.16091717X-RAY DIFFRACTION97
3.6919-4.22350.17971810.14361751X-RAY DIFFRACTION97
4.2235-5.31110.14281850.12311776X-RAY DIFFRACTION98
5.3111-23.6070.19151960.15931879X-RAY DIFFRACTION98

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