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- PDB-3vxj: Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol -

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Basic information

Entry
Database: PDB / ID: 3vxj
TitleDye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol
ComponentsDyP
KeywordsOXIDOREDUCTASE / DyP / Dye-decolorizing peroxidase / 2 / 6-dimethoxyphenol
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / DyP dimeric alpha+beta barrel domain / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
2,6-dimethoxyphenol / PROTOPORPHYRIN IX CONTAINING FE / DyP
Similarity search - Component
Biological speciesBjerkandera adusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsSugano, Y. / Yoshida, T. / Tsuge, H.
CitationJournal: to be published
Title: Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol
Authors: Sugano, Y. / Yoshida, T. / Tsuge, H.
History
DepositionSep 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DyP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7216
Polymers47,4971
Non-polymers1,2245
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.167, 96.344, 49.778
Angle α, β, γ (deg.)90.000, 106.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein DyP / dye-decolorizing peroxidase


Mass: 47497.344 Da / Num. of mol.: 1 / Fragment: UNP residues 57-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bjerkandera adusta (fungus) / Strain: Dec 1 / Gene: dyp / Plasmid: pTAex3 / Production host: Aspergillus oryzae (mold) / Strain (production host): M-2-3 / References: UniProt: Q8WZK8, dye decolorizing peroxidase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 169 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-3DM / 2,6-dimethoxyphenol


Mass: 154.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.68 % / Mosaicity: 1.223 °
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, pH 6.0, vapor diffusion, hanging drop, temperature 278K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 36.86 / Number: 284023 / Rmerge(I) obs: 0.049 / Χ2: 2.08 / D res high: 1.39 Å / D res low: 50 Å / Num. obs: 77992 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.775082.510.0332.083.4
2.993.7792.610.0311.8783.6
2.622.9998.410.0341.8243.7
2.382.6298.410.041.9573.8
2.212.3898.210.0432.0683.8
2.082.219810.0492.2543.7
1.972.0897.510.0562.353.7
1.891.9797.610.0652.4033.7
1.811.8997.210.0742.3523.7
1.751.8197.110.0862.2713.7
1.71.7596.710.0962.183.7
1.651.796.410.1122.1263.6
1.61.6596.610.1262.1483.6
1.571.69610.142.0433.6
1.531.5795.810.1592.1083.6
1.51.5395.310.1831.9883.6
1.471.595.310.2021.9283.6
1.441.4795.310.2221.9053.5
1.411.4495.310.2461.7583.5
1.391.4194.910.2831.8063.5
ReflectionResolution: 1.39→50 Å / Num. obs: 77992 / % possible obs: 95.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.049 / Χ2: 2.076 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.39-1.413.50.28338841.806194.9
1.41-1.443.50.24638151.758195.3
1.44-1.473.50.22238961.905195.3
1.47-1.53.60.20238831.928195.3
1.5-1.533.60.18338461.988195.3
1.53-1.573.60.15939072.108195.8
1.57-1.63.60.1439042.043196
1.6-1.653.60.12638952.148196.6
1.65-1.73.60.11239042.126196.4
1.7-1.753.70.09639572.18196.7
1.75-1.813.70.08639342.271197.1
1.81-1.893.70.07439562.352197.2
1.89-1.973.70.06539872.403197.6
1.97-2.083.70.05639672.35197.5
2.08-2.213.70.04939712.254198
2.21-2.383.80.04340302.068198.2
2.38-2.623.80.0440111.957198.4
2.62-2.993.70.03440211.824198.4
2.99-3.773.60.03137981.878192.6
3.77-503.40.03334262.08182.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å24.51 Å
Translation3 Å24.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFV

3afv


Resolution: 1.39→48.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1913 / WRfactor Rwork: 0.1759 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8957 / SU B: 1.547 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0634 / SU Rfree: 0.0615 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 3880 5 %RANDOM
Rwork0.1802 ---
obs0.1809 77869 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 34.81 Å2 / Biso mean: 12.763 Å2 / Biso min: 2.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20.38 Å2
2---0.85 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.39→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 83 165 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223508
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9964798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00824.908163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55815494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8331516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212788
LS refinement shellResolution: 1.391→1.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 281 -
Rwork0.234 5206 -
all-5487 -
obs--91.89 %
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)
11.6938-0.2015-0.74812.3171-1.86183.99650.0141-0.20470.08320.35360.0147-0.024-0.30290.1056-0.02880.0551-0.0115-0.02290.0606-0.00180.043712.0707-7.603228.2671
21.12770.37480.07241.9608-0.41920.91630.019-0.00560.0246-0.0445-0.02590.00040.02080.05560.00690.02170.01140.00020.07490.00110.057515.066-13.367210.9918
30.5903-0.4229-0.7724.29591.65411.1421-0.0063-0.1335-0.03350.12690.0176-0.25880.05430.208-0.01130.01370.0083-0.0350.09960.02510.057420.7006-15.778720.9823
49.78921.3457-7.0118-0.46983.49430.4433-0.1541-0.62761.19360.29530.10290.2547-0.13652.3960.05120.1219-0.1768-0.12120.19460.06790.141824.5975-1.962224.7583
50.7337-0.0271-0.43890.2534-0.16040.6028-0.0309-0.0004-0.08820.0282-0.01140.01260.0717-0.00340.04230.03510.0034-0.00690.04050.00460.05634.792-18.941816.55
60.8257-0.34950.05221.45190.05870.44070.04730.087-0.0127-0.1694-0.05230.0356-0.0026-0.03890.0050.04110.0025-0.01560.051-0.0190.0394-3.0658-10.36174.0217
70.56330.1017-0.08640.7628-0.01210.33160.00020.02080.0245-0.0498-0.0058-0.07630.0220.0520.00550.0156-0.0006-0.00870.06180.00160.055918.5978-8.19778.3479
80.55080.258-0.69661.26380.15060.75530.0075-0.1722-0.07550.2155-0.0808-0.1590.08270.1870.07330.036-0.0014-0.02960.08410.01350.05767.35797.182922.4743
90.69530.3692-0.03071.4889-0.33690.4997-0.0109-0.07480.01780.14470.01290.0294-0.03340.0107-0.00190.0387-0.0015-0.00640.04690.00210.0351.0786-10.612128.1267
100.3263-0.33560.06492.7515-1.32490.80330.04250.08110.0046-0.1679-0.0748-0.0232-0.01190.00970.03220.05380.0097-0.00680.0577-0.00330.02362.1646.38582.3655
110.3426-0.1544-0.03380.9311-0.23520.57430.00840.0070.04150.0259-0.026-0.031-0.07980.05140.01770.0287-0.0066-0.00510.0393-0.00120.0349-2.712819.555916.2544
120.6314-0.22360.0530.8428-0.00040.3510.01520.04680.0306-0.0414-0.0174-0.0012-0.04460.02250.00220.0375-0.0021-0.0130.0478-0.00520.0448-0.743.066112.4348
130.6699-0.477-0.26681.00970.37710.63710.02860.0457-0.0453-0.1047-0.040.117-0.0265-0.04850.01140.02090.0028-0.02050.0468-0.0010.0512-12.204412.85928.2171
140.6218-0.22030.30351.0345-0.57061.29850.0226-0.0139-0.0714-0.0234-0.0367-0.04710.08950.07380.01410.03060.0018-0.00170.054-0.00580.05987.2444-14.876916.4182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 18
2X-RAY DIFFRACTION2A19 - 38
3X-RAY DIFFRACTION3A39 - 54
4X-RAY DIFFRACTION4A55 - 65
5X-RAY DIFFRACTION5A66 - 89
6X-RAY DIFFRACTION6A90 - 115
7X-RAY DIFFRACTION7A116 - 161
8X-RAY DIFFRACTION8A162 - 188
9X-RAY DIFFRACTION9A189 - 218
10X-RAY DIFFRACTION10A219 - 233
11X-RAY DIFFRACTION11A234 - 315
12X-RAY DIFFRACTION12A316 - 381
13X-RAY DIFFRACTION13A382 - 420
14X-RAY DIFFRACTION14A421 - 442

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