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- PDB-2dki: Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas... -

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Basic information

Entry
Database: PDB / ID: 2dki
TitleCrystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, under pressure of xenon gas (12 atm)
Components3-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE / 3-HYDROXYBENZOATE HYDROXYLASE / FLAVOPROTEIN / MONOOXYGENASE / XENON DERIVATIVE
Function / homology
Function and homology information


3-hydroxybenzoate 4-monooxygenase / 3-hydroxybenzoate 4-monooxygenase activity / FAD binding / protein homodimerization activity
Similarity search - Function
Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal TRX-fold domain superfamily / Phenol hydroxylase, C-terminal dimerisation domain / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain ...Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal TRX-fold domain superfamily / Phenol hydroxylase, C-terminal dimerisation domain / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / XENON / 3-hydroxybenzoate 4-monooxygenase / 3-hydroxybenzoate 4-monooxygenase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHiromoto, T. / Fujiwara, S. / Hosokawa, K. / Yamaguchi, H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site
Authors: Hiromoto, T. / Fujiwara, S. / Hosokawa, K. / Yamaguchi, H.
History
DepositionApr 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: 3-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0528
Polymers70,5841
Non-polymers1,4687
Water6,846380
1
A: 3-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: 3-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,10316
Polymers141,1682
Non-polymers2,93514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area10230 Å2
ΔGint-125 kcal/mol
Surface area46010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.680, 73.680, 224.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-984-

HOH

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Components

#1: Protein 3-HYDROXYBENZOATE HYDROXYLASE / m-hydroxybenzoate hydroxylase


Mass: 70584.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / Strain: KH122-3s
References: UniProt: Q05KQ5, UniProt: Q6SSJ6*PLUS, 3-hydroxybenzoate 4-monooxygenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 1.3M AMMONIUM SULFATE, 6% 1,4-DIOXANE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2001 / Details: PT-COATED BENT CYLINDRICAL MIRROR OF FUSED QUARTZ
RadiationMonochromator: FIXED-EXIT DOUBLE-CRYSTAL MONOCHROMATOR WITH GE(111) CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 25436 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 11 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3652 / Rsym value: 0.271 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DKH

2dkh


Resolution: 2.5→35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1975911.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.001 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2508 9.9 %RANDOM
Rwork0.177 ---
obs0.177 25332 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.46 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å23.92 Å20 Å2
2--3.38 Å20 Å2
3----7.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 71 380 5247
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it3.371.5
X-RAY DIFFRACTIONc_mcangle_it4.672
X-RAY DIFFRACTIONc_scbond_it5.252
X-RAY DIFFRACTIONc_scangle_it6.542.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 411 9.9 %
Rwork0.21 3731 -
obs-3731 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD_14.PARAMFAD_14.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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