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- PDB-2jbr: Structure of the monooxygenase component of p-hydroxyphenylacetat... -

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Basic information

Entry
Database: PDB / ID: 2jbr
TitleStructure of the monooxygenase component of p-hydroxyphenylacetate hydroxylase from Acinetobacter baumanni
ComponentsP-HYDROXYPHENYLACETATE HYDROXYLASE C2 OXYGENASE COMPONENT
KeywordsOXIDOREDUCTASE / FLAVOENZYME HYDROXYLASE
Function / homology
Function and homology information


4-hydroxyphenylacetate 3-monooxygenase / 4-hydroxyphenylacetate 3-monooxygenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / : / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
p-hydroxyphenylacetate 3-hydroxylase, oxygenase component
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsAlfieri, A. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure of the Monooxygenase Component of a Two-Component Flavoprotein Monooxygenase.
Authors: Alfieri, A. / Fersini, F. / Ruangchan, N. / Prongjit, M. / Chaiyen, P. / Mattevi, A.
History
DepositionDec 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-HYDROXYPHENYLACETATE HYDROXYLASE C2 OXYGENASE COMPONENT
B: P-HYDROXYPHENYLACETATE HYDROXYLASE C2 OXYGENASE COMPONENT
C: P-HYDROXYPHENYLACETATE HYDROXYLASE C2 OXYGENASE COMPONENT
D: P-HYDROXYPHENYLACETATE HYDROXYLASE C2 OXYGENASE COMPONENT


Theoretical massNumber of molelcules
Total (without water)188,0104
Polymers188,0104
Non-polymers00
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.441, 182.077, 287.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A24 - 33
2111B24 - 33
3111C24 - 33
4111D24 - 33
1211A39 - 185
2211B39 - 185
3211C39 - 185
4211D39 - 185
1311A192 - 292
2311B192 - 292
3311C192 - 292
4311D192 - 292
1411A301 - 422
2411B301 - 422
3411C301 - 422
4411D301 - 422

NCS oper:
IDCodeMatrixVector
1given(-0.76966, -0.00969, 0.63838), (-0.02086, -0.99897, -0.04032), (0.63811, -0.04435, 0.76867)-5.63282, 67.23197, 3.59378
2given(-0.11269, -0.93412, -0.33871), (-0.93216, -0.01865, 0.36158), (-0.34407, 0.35648, -0.86864)99.66084, 26.15179, 187.25813
3given(-0.11328, 0.94829, -0.29651), (0.94782, 0.01363, -0.31851), (-0.298, -0.31712, -0.90035)36.61334, 31.55933, 209.97333

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Components

#1: Protein
P-HYDROXYPHENYLACETATE HYDROXYLASE C2 OXYGENASE COMPONENT


Mass: 47002.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6Q272
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 3.32 Å3/Da / Density % sol: 62.72 %
Crystal growpH: 6.8 / Details: pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 105406 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→71.07 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.443 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1060 1 %RANDOM
Rwork0.218 ---
obs0.218 104334 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12472 0 0 375 12847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.94617264
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32951591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44223.833587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.465152144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5011579
X-RAY DIFFRACTIONr_chiral_restr0.0960.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.26085
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.28812
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6211.58202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.053212674
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.535294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4644.54590
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2974 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.020.05
4Dtight positional0.020.05
1Atight thermal0.050.5
2Btight thermal0.050.5
3Ctight thermal0.040.5
4Dtight thermal0.040.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 74
Rwork0.323 7050
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)
10.9582-0.02560.0671.1097-0.42440.5576-0.0152-0.10590.1183-0.0268-0.0243-0.0334-0.03010.18630.0395-0.0697-0.02020.0136-0.22460.0168-0.110932.603250.773480.6682
20.7606-0.0889-0.18520.86070.28130.6552-0.0319-0.1913-0.2167-0.0070.00950.01650.12350.02220.0224-0.04520.02450.0004-0.26740.0713-0.021920.315412.474784.1809
31.3591-0.0383-0.41330.07050.25161.3432-0.0231-0.7317-0.2072-0.0194-0.0258-0.12230.16630.11750.0489-0.07210.0501-0.0050.38880.1783-0.156221.233323.9826124.0629
41.82460.19450.06780.6745-0.36170.9837-0.0147-0.6175-0.05380.1082-0.1145-0.2547-0.07930.57710.1293-0.1022-0.0102-0.05390.54870.0702-0.016457.153637.4648111.5232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 422
2X-RAY DIFFRACTION2B24 - 422
3X-RAY DIFFRACTION3C24 - 422
4X-RAY DIFFRACTION4D24 - 422

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