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- PDB-2qa2: Crystal structure of CabE, an aromatic hydroxylase from angucycli... -

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Basic information

Entry
Database: PDB / ID: 2qa2
TitleCrystal structure of CabE, an aromatic hydroxylase from angucycline biosynthesis, determined to 2.7 A resolution
ComponentsPolyketide oxygenase CabE
KeywordsOXIDOREDUCTASE / FAD / angucycline / polyketide / aromatic hydroxylase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding
Similarity search - Function
Alpha-Beta Plaits - #2450 / Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin ...Alpha-Beta Plaits - #2450 / Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Polyketide oxygenase CabE
Similarity search - Component
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKoskiniemi, H. / Dobritzsch, D. / Metsa-Ketela, M. / Kallio, P. / Niemi, J. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of two aromatic hydroxylases involved in the early tailoring steps of angucycline biosynthesis
Authors: Koskiniemi, H. / Metsa-Ketela, M. / Dobritzsch, D. / Kallio, P. / Korhonen, H. / Mantsala, P. / Schneider, G. / Niemi, J.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Polyketide oxygenase CabE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4252
Polymers53,6391
Non-polymers7861
Water43224
1
A: Polyketide oxygenase CabE
hetero molecules

A: Polyketide oxygenase CabE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8504
Polymers107,2792
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5190 Å2
ΔGint-39 kcal/mol
Surface area40170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.100, 133.100, 166.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological unit is a dimer generated from the monomer in the asymmetric unit by the operation 1 0 0 0-1 0 0 0-1

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Components

#1: Protein Polyketide oxygenase CabE / E.C.1.14.13.- / CabE / aromatic hydroxylase


Mass: 53639.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Genus: Streptomyces / Strain: sp. H021 / Gene: cabe / Plasmid: pBHB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: D0VWY3*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of ...References: UniProt: D0VWY3*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.98 Å3/Da / Density % sol: 69.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG 3350, 0.1M bis-tris propane, 0.2M Na/K-phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2006
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 24379 / Num. obs: 24379 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 16.22
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4 / Num. unique all: 2467 / Rsym value: 0.518 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QA1

2qa1


Resolution: 2.7→29.83 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 35.281 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.437 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The analysis of the intensity distribution suggests possible twinning. Refinement using the twin protocol did however not improve Rfree and the crystals were therefore not considered twinned ...Details: The analysis of the intensity distribution suggests possible twinning. Refinement using the twin protocol did however not improve Rfree and the crystals were therefore not considered twinned with space group P6522. Furthermore, data processing using programs other than XDS did not show signs of twinning.
RfactorNum. reflection% reflectionSelection details
Rfree0.27428 1220 5 %RANDOM
Rwork0.23428 ---
all0.23633 23190 --
obs0.23633 23190 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.281 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å2-1.35 Å20 Å2
2---2.71 Å20 Å2
3---4.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 53 24 3752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9845199
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66122.156167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13615579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5251545
X-RAY DIFFRACTIONr_chiral_restr0.090.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022964
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21752
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22542
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.76822474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32133864
X-RAY DIFFRACTIONr_scbond_it1.03431541
X-RAY DIFFRACTIONr_scangle_it1.60741334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 88 -
Rwork0.377 1671 -
obs-88 99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.98032.5301-0.65018.0094-2.28752.40290.0855-0.1096-0.30740.7022-0.13480.23960.12570.02950.0493-0.1733-0.02470.1976-0.6230.0555-0.4498-33.358-23.6611.521
29.8472.17252.11287.52331.31419.9929-0.3631-0.0276-0.57770.58-0.1833-0.0911-0.69470.03880.54650.5219-0.42140.1948-0.0286-0.1157-0.1462-17.276-4.5919.967
36.26851.1405-1.08076.20751.38665.4308-0.11340.80140.3971-0.25430.23261.68660.1931-0.9792-0.1191-0.0504-0.11280.1833-0.21450.22340.6499-58.612-28.2818.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 17211 - 182
2X-RAY DIFFRACTION1AC5001
3X-RAY DIFFRACTION1AA255 - 373265 - 383
4X-RAY DIFFRACTION2AA173 - 254183 - 264
5X-RAY DIFFRACTION3AA374 - 489384 - 499

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