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- PDB-8r2t: Crystal structure of 4-hydroxybenzoate-1-hydroxylase from Gelatop... -

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Basic information

Entry
Database: PDB / ID: 8r2t
TitleCrystal structure of 4-hydroxybenzoate-1-hydroxylase from Gelatoporia subvermispora (GsMNX1)
ComponentsFAD-binding domain-containing protein
KeywordsOXIDOREDUCTASE / fungi / oxidative decarboxylase
Function / homology: / FAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / FAD-binding domain-containing protein
Function and homology information
Biological speciesGelatoporia subvermispora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.824 Å
AuthorsZahn, M. / Kuatsjah, E. / Salvachua, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 United Kingdom
CitationJournal: Cell Rep / Year: 2024
Title: Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi.
Authors: Kuatsjah, E. / Schwartz, A. / Zahn, M. / Tornesakis, K. / Kellermyer, Z.A. / Ingraham, M.A. / Woodworth, S.P. / Ramirez, K.J. / Cox, P.A. / Pickford, A.R. / Salvachua, D.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-binding domain-containing protein
B: FAD-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7806
Polymers106,1382
Non-polymers1,6424
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-41 kcal/mol
Surface area29820 Å2
Unit cell
Length a, b, c (Å)112.216, 64.789, 160.100
Angle α, β, γ (deg.)90.000, 93.896, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 18 - 464 / Label seq-ID: 18 - 464

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein FAD-binding domain-containing protein


Mass: 53068.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gelatoporia subvermispora (fungus) / Gene: CERSUDRAFT_120062 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2QGN5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: LMB screen from Molecular Dimensions condition G7 (11% PEG 8000, 0.4 M sodium chloride, 0.1 M sodium cacodylate pH 6.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.824→159.73 Å / Num. obs: 57625 / % possible obs: 92.7 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.075 / Net I/σ(I): 6.5
Reflection shellResolution: 1.824→2.108 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.016 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2881 / CC1/2: 0.786 / Rpim(I) all: 0.434 / % possible all: 58.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.824→159.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.385 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2246 2912 5.053 %
Rwork0.1789 54713 -
all0.181 --
obs-57625 56.314 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.395 Å2
2---0.03 Å20 Å2
3---0.034 Å2
Refinement stepCycle: LAST / Resolution: 1.824→159.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6409 0 108 379 6896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166323
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6529098
X-RAY DIFFRACTIONr_angle_other_deg0.5051.57314492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.78564
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.02852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.916101076
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.04910303
X-RAY DIFFRACTIONr_chiral_restr0.0730.2992
X-RAY DIFFRACTIONr_chiral_restr_other0.0140.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021589
X-RAY DIFFRACTIONr_nbd_refined0.2080.21324
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26033
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23246
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23707
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2404
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.211
X-RAY DIFFRACTIONr_nbd_other0.1940.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.212
X-RAY DIFFRACTIONr_mcbond_it1.9832.2453309
X-RAY DIFFRACTIONr_mcbond_other1.9822.2453309
X-RAY DIFFRACTIONr_mcangle_it3.084.0164126
X-RAY DIFFRACTIONr_mcangle_other3.084.0164127
X-RAY DIFFRACTIONr_scbond_it2.5392.4373384
X-RAY DIFFRACTIONr_scbond_other2.5372.4363381
X-RAY DIFFRACTIONr_scangle_it3.9194.3654968
X-RAY DIFFRACTIONr_scangle_other3.9194.3654969
X-RAY DIFFRACTIONr_lrange_it5.82621.5567770
X-RAY DIFFRACTIONr_lrange_other5.79721.4477696
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0513344
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088530.05008
12AX-RAY DIFFRACTIONLocal ncs0.088530.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.824-1.8710.38740.311580.31475040.9210.9420.82620.297
1.871-1.9230.354100.2181520.22573510.9440.9692.20380.216
1.923-1.9780.242220.244150.2471480.9650.9636.11360.23
1.978-2.0390.279400.2478210.24969440.9460.9612.39920.236
2.039-2.1060.247560.24712560.24766950.9640.95219.59670.229
2.106-2.180.251960.23718770.23864870.9580.96330.41470.224
2.18-2.2620.2471540.24127780.24162930.9550.96346.59150.223
2.262-2.3550.2731990.23138040.23360390.950.96566.28580.21
2.355-2.4590.2322230.22543460.22557920.9640.96878.88470.201
2.459-2.5790.2612410.20747030.2155860.9610.97388.5070.183
2.579-2.7190.2612690.20649010.20952900.9540.97497.73160.181
2.719-2.8840.2882810.19546960.249770.9530.9761000.173
2.884-3.0830.2492740.18744670.19147410.9590.9791000.169
3.083-3.330.2072230.17641300.17843530.9750.9821000.163
3.33-3.6470.2171820.1738850.17240670.9740.9841000.163
3.647-4.0780.2131820.1534930.15336750.9780.9871000.151
4.078-4.7080.1611570.12930830.1332400.9850.991000.134
4.708-5.7650.2061460.15526070.15827530.9790.9881000.161
5.765-8.1470.204910.17320820.17421730.9790.9831000.18
8.147-159.730.202620.17311590.17412210.9620.9611000.196
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)
11.140.20190.6210.42290.13870.8345-0.0430.07560.029-0.05110.0194-0.0512-0.0218-0.01240.02360.0336-0.00220.040.01110.0020.053611.03190.73665.1534
20.33610.03540.18250.5621-0.14891.06570.00670.2141-0.0731-0.24640.01070.13730.0685-0.1211-0.01740.2122-0.0209-0.01670.2939-0.04980.1519-10.3049-19.498825.6877
Refinement TLS groupSelection: ALL

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