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

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Basic information

Entry
Database: PDB / ID: 4lbh
Title5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burkholderia phenoliruptrix AC1100: Apo-form
Components5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
KeywordsLYASE
Function / homologyYCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / YCII-related domain-containing protein
Function and homology information
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2882
Polymers11,1821
Non-polymers1061
Water1,42379
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)45,1518
Polymers44,7274
Non-polymers4244
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 area8000 Å2
ΔGint-9 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.317, 90.317, 51.256
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-322-

HOH

21A-342-

HOH

31A-352-

HOH

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Components

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


Mass: 11181.664 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
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: Jan 28, 2013
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: 1.75→50 Å / Num. all: 12883 / Num. obs: 12883 / % possible obs: 99.6 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.75-1.781100
1.78-1.811100
1.81-1.851100
1.85-1.891100
1.89-1.931100

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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: 1.75→45.158 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1277 9.96 %RANDOM
Rwork0.1859 ---
obs0.189 12826 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→45.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 7 79 823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007773
X-RAY DIFFRACTIONf_angle_d1.0781043
X-RAY DIFFRACTIONf_dihedral_angle_d11.766283
X-RAY DIFFRACTIONf_chiral_restr0.076111
X-RAY DIFFRACTIONf_plane_restr0.004134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.82050.21891380.21721232X-RAY DIFFRACTION97
1.8205-1.90340.24951360.1911239X-RAY DIFFRACTION99
1.9034-2.00370.2561360.20071253X-RAY DIFFRACTION99
2.0037-2.12930.22441390.17921264X-RAY DIFFRACTION100
2.1293-2.29370.22611380.18491257X-RAY DIFFRACTION99
2.2937-2.52450.25081430.18151290X-RAY DIFFRACTION100
2.5245-2.88970.22271440.1841291X-RAY DIFFRACTION100
2.8897-3.64050.20921460.18061313X-RAY DIFFRACTION100
3.6405-45.1580.19261570.18651410X-RAY DIFFRACTION99

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