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- PDB-3vsg: Crystal structure of iron free 1,6-APD, 2-Animophenol-1,6-Dioxygenase -

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Basic information

Entry
Database: PDB / ID: 3vsg
TitleCrystal structure of iron free 1,6-APD, 2-Animophenol-1,6-Dioxygenase
Components
  • 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit
  • 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit
KeywordsOXIDOREDUCTASE / EXTRADIOL DIOXYGENASE / CNBC / 2-HIS-1-CARBOXYLATE FACIAL TRIAD MOTIF
Function / homology
Function and homology information


2-amino-5-chlorophenol 1,6-dioxygenase / 2-aminophenol 1,6-dioxygenase / dioxygenase activity / catabolic process / ferrous iron binding
Similarity search - Function
2-aminophenol 1,6-dioxygenase, beta subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-aminophenol 1,6-dioxygenase subunit alpha / 2-aminophenol 1,6-dioxygenase subunit beta / 2-aminophenol 1,6-dioxygenase subunit alpha / 2-aminophenol 1,6-dioxygenase subunit beta
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsLi, D.F. / Hou, Y.J. / Hu, Y. / Wang, D.C. / Liu, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor
Authors: Li, D.F. / Zhang, J.Y. / Hou, Y.J. / Liu, L. / Hu, Y. / Liu, S.J. / Wang, D.C. / Liu, W.
History
DepositionApr 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit
B: 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit
C: 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit
D: 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit


Theoretical massNumber of molelcules
Total (without water)128,7624
Polymers128,7624
Non-polymers00
Water23,6001310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-27 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)269.730, 48.260, 108.440
Angle α, β, γ (deg.)90.00, 109.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit


Mass: 29298.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / Strain: CNB-1
References: UniProt: Q38M40, UniProt: Q6J1Z5*PLUS, protocatechuate 4,5-dioxygenase
#2: Protein 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit


Mass: 35083.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / Strain: CNB-1
References: UniProt: Q38M41, UniProt: Q6J1Z6*PLUS, protocatechuate 4,5-dioxygenase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1310 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
SYNCHROTRONPhoton Factory AR-NW12A20.9792, 0.9794, 0.9642
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEApr 25, 2007MIRRORS
ADSC QUANTUM 2102CCDJun 15, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97921
30.97941
40.96421
ReflectionResolution: 2.4→39.78 Å / Num. all: 52295 / Num. obs: 48049 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 20.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.323 / % possible all: 82.5

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Processing

Software
NameClassification
CrystalCleardata collection
SnBphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→39.78 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2271 4.3 %RANDOM
Rwork0.186 ---
obs0.186 45191 86.4 %-
all-52295 --
Solvent computationBsol: 37.36 Å2
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.204 Å20 Å2-2.785 Å2
2---2.293 Å20 Å2
3----0.911 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8905 0 0 1310 10215
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.31
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 174 -
Rwork0.292 --
obs--73 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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