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- PDB-5vj0: Crystal Structure of heme-containing DyP Type Peroxidase from Ent... -

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Basic information

Entry
Database: PDB / ID: 5vj0
TitleCrystal Structure of heme-containing DyP Type Peroxidase from Enterobacter lignolyticus
ComponentsDyp-type peroxidase family
KeywordsOXIDOREDUCTASE / Enterobacter lignolyticus / Peroxidase / Heme / Lignin
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / 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
PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family
Similarity search - Component
Biological speciesEnterobacter lignolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMeekins, D.A. / Li, P. / Geisbrecht, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117259 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121511 United States
CitationJournal: ACS Catal / Year: 2017
Title: Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects.
Authors: Shrestha, R. / Huang, G. / Meekins, D.A. / Geisbrecht, B.V. / Li, P.
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dyp-type peroxidase family
B: Dyp-type peroxidase family
C: Dyp-type peroxidase family
D: Dyp-type peroxidase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1498
Polymers141,6834
Non-polymers2,4664
Water20,5731142
1
A: Dyp-type peroxidase family
B: Dyp-type peroxidase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0754
Polymers70,8422
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-61 kcal/mol
Surface area23710 Å2
MethodPISA
2
C: Dyp-type peroxidase family
D: Dyp-type peroxidase family
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, Protein Exists as a Dimer in Solution, According to Analytical Gel-Filtration Chromatography. EBI-PISA Interface/Assembly Analysis Suggests Biological Dimer is Comprised of Chains A/B and C/D
  • 72.1 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)72,0754
Polymers70,8422
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-60 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.870, 74.160, 118.640
Angle α, β, γ (deg.)90.000, 108.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dyp-type peroxidase family


Mass: 35420.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter lignolyticus (bacteria) / Gene: YfeX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3G9I4
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1M HEPES, pH 7.3, 25% (v/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2016
RadiationMonochromator: Si (220) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→43.449 Å / Num. obs: 92368 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 7.755 % / Biso Wilson estimate: 23.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.077 / Χ2: 0.966 / Net I/σ(I): 19.45 / Num. measured all: 716348 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.93-1.987.8380.6083.8352821695767390.9180.65196.9
1.98-2.037.8320.4594.9151364676565580.9550.49196.9
2.03-2.097.8260.3935.7849998657663890.9610.42197.2
2.09-2.167.8270.326.8548757640462290.9720.34397.3
2.16-2.237.8250.2618.2547121617960220.9810.27997.5
2.23-2.317.820.2119.9245739600158490.9860.22697.5
2.31-2.397.8160.18311.3244075576556390.990.19697.8
2.39-2.497.8070.15113.1942633557654610.9920.16297.9
2.49-2.67.7980.12415.6540908535152460.9950.13398
2.6-2.737.7850.10118.5839203512850360.9960.10898.2
2.73-2.887.7790.08122.2537128485347730.9980.08798.4
2.88-3.057.750.06526.6335268461545510.9980.0798.6
3.05-3.267.7360.05531.3433024433342690.9990.05898.5
3.26-3.527.6720.04637.1830697404740010.9990.04998.9
3.52-3.867.6470.03941.8628096371036740.9990.04299
3.86-4.327.5970.03546.4725443338133490.9990.03799.1
4.32-4.987.5690.03349.2322518299929750.9990.03599.2
4.98-6.17.5440.03447.1219078254525290.9990.03799.4
6.1-8.637.4060.03448.5414545197819640.9990.03699.3
8.63-43.4497.1140.03253.17932113411150.9980.03598.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DE0

5de0


Resolution: 1.93→43.449 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1992 2.25 %
Rwork0.1726 86634 -
obs0.1733 88626 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.11 Å2 / Biso mean: 30.3995 Å2 / Biso min: 10.73 Å2
Refinement stepCycle: final / Resolution: 1.93→43.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 0 172 1142 10604
Biso mean--24.39 34.01 -
Num. residues----1194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069687
X-RAY DIFFRACTIONf_angle_d0.84713149
X-RAY DIFFRACTIONf_chiral_restr0.0481374
X-RAY DIFFRACTIONf_plane_restr0.0041719
X-RAY DIFFRACTIONf_dihedral_angle_d14.9233475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.97820.28571340.23685542567684
1.9782-2.03170.24021310.21995760589188
2.0317-2.09150.22721400.21225867600790
2.0915-2.1590.23411380.20636042618092
2.159-2.23620.24131380.19865994613292
2.2362-2.32570.22131420.19366107624993
2.3257-2.43150.23341430.1926167631094
2.4315-2.55970.22931440.19566260640495
2.5597-2.72010.22791420.19186329647196
2.7201-2.93010.23161420.18926369651197
2.9301-3.22480.22831490.18666433658298
3.2248-3.69130.19271450.16386508665399
3.6913-4.64970.15221500.13096566671699
4.6497-43.45990.15651540.14366690684499

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