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- PDB-9lft: Biochemical and structural characterization of a novel 4-hydroxyp... -

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Basic information

Entry
Database: PDB / ID: 9lft
TitleBiochemical and structural characterization of a novel 4-hydroxyphenylacetate-3-monooxygenase from Geobacillus mahadii Geo-05
Components4-Hydroxyphenylacetate-3-monooxygenase
KeywordsHYDROLASE / Hydroxylation / two-component monooxygenases / thermophilic enzyme / flavoprotein
Biological speciesGeobacillus mahadia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChe Husain, N.A. / Jamaluddin, H. / Jonet, M.A. / Padzil, A.M. / Taib, A.Z.M. / Zain, N.C. / Bakar, M.F.A. / Acharya, K.R. / Gregory, K.S.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Other governmentFRGS/1/2019/STG05/MOSTI/02/1 Malaysia
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Biochemical and structural insights into GMHpaB: A thermostable 4-Hydroxyphenylacetate-3-monooxygenase with dual cofactor versatility.
Authors: Che Husain, N.A. / Padzil, A.M. / Taib, A.Z.M. / Zain, N.C. / Bakar, M.F.A. / Gregory, K.S. / Acharya, K.R. / Jonet, M.A. / Jamaluddin, H.
History
DepositionJan 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-Hydroxyphenylacetate-3-monooxygenase
B: 4-Hydroxyphenylacetate-3-monooxygenase
C: 4-Hydroxyphenylacetate-3-monooxygenase
D: 4-Hydroxyphenylacetate-3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,4415
Polymers235,2194
Non-polymers1,2211
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27850 Å2
ΔGint-179 kcal/mol
Surface area58190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.571, 108.202, 99.055
Angle α, β, γ (deg.)90.00, 99.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-Hydroxyphenylacetate-3-monooxygenase


Mass: 58804.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus mahadia (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: 4-hydroxyphenylacetate 3-monooxygenase
#2: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.8M Sodium formate, 0.1M Sodium cacodylate, 25% w/v PEG200 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953738 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953738 Å / Relative weight: 1
ReflectionResolution: 2.4→108.2 Å / Num. obs: 73743 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.078 / Rrim(I) all: 0.203 / Χ2: 0.9 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.262 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4549 / CC1/2: 0.589 / Rpim(I) all: 0.801 / Rrim(I) all: 1.389 / Χ2: 0.92 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→97.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.463 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.643 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24989 3637 4.9 %RANDOM
Rwork0.18398 ---
obs0.18714 70078 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.125 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20.11 Å2
2---1.03 Å20 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.4→97.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15417 0 76 121 15614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01215853
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614779
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.82921424
X-RAY DIFFRACTIONr_angle_other_deg0.5871.75933966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90751926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.1655136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.986102660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023855
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it1.6552.5977716
X-RAY DIFFRACTIONr_mcbond_other1.6552.5977717
X-RAY DIFFRACTIONr_mcangle_it2.5284.6699638
X-RAY DIFFRACTIONr_mcangle_other2.5284.6699639
X-RAY DIFFRACTIONr_scbond_it2.2682.8678137
X-RAY DIFFRACTIONr_scbond_other2.2682.8678138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6125.14411787
X-RAY DIFFRACTIONr_long_range_B_refined4.54325.6817603
X-RAY DIFFRACTIONr_long_range_B_other4.54325.6817598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 265 -
Rwork0.266 5145 -
obs--99.61 %
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)
10.6593-0.1452-0.0610.3135-0.24461.07690.0420.1709-0.0012-0.1656-0.0486-0.0460.1360.1210.00660.08940.01640.02580.064-0.0040.009138.506-3.28410.841
20.7063-0.033-0.06310.847-0.2750.42510.01580.02120.1464-0.01410.00420.0805-0.0998-0.0705-0.020.03750.0192-0.00530.01530.00070.04091.91510.59816.4
30.59830.19750.03670.2872-0.0740.62240.0442-0.08710.03330.1099-0.02080.0537-0.0364-0.021-0.02330.07690.00460.02790.015-0.00120.012230.884-14.19851.118
40.69170.08370.23450.8941-0.29490.76620.03750.0205-0.1789-0.07210.02920.11620.234-0.099-0.06670.0773-0.0313-0.00080.0199-0.00360.0827-1.5-27.59233.952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 481
2X-RAY DIFFRACTION2B1 - 485
3X-RAY DIFFRACTION3C1 - 480
4X-RAY DIFFRACTION3B601
5X-RAY DIFFRACTION4D1 - 484

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