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- PDB-7e5q: Crystal Structure of Dye Decolorizing peroxidase from Bacillus su... -

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Basic information

Entry
Database: PDB / ID: 7e5q
TitleCrystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis at acidic pH
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / Dye-decolorizing peroxidase / ferredoxin like fold / heme / acidic
Function / homology
Function and homology information


iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / membrane => GO:0016020 / heme binding / metal ion binding
Similarity search - Function
TAT (twin-arginine translocation) pathway signal sequence / Deferrochelatase / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
CITRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / Deferrochelatase/peroxidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDhankhar, P. / Dalal, V. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT-1088-BIO India
CitationJournal: Proteins / Year: 2022
Title: Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis.
Authors: Dhankhar, P. / Dalal, V. / Sharma, A.K. / Kumar, P.
History
DepositionFeb 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase/peroxidase
B: Deferrochelatase/peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,18347
Polymers80,4712
Non-polymers3,71245
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-171 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.855, 117.342, 135.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Deferrochelatase/peroxidase


Mass: 40235.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: efeB, GS595_16230 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6G2J275, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 9 types, 613 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M Sodium citrate, 1M LiCl, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.9→44.344 Å / Num. obs: 52281 / % possible obs: 99.37 % / Redundancy: 6.8 % / CC1/2: 0.98 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.96 Å / Num. unique obs: 7225 / CC1/2: 0.89 / % possible all: 5.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KMM

6kmm


Resolution: 1.9→44.344 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 2000 3.84 %RANDOM
Rwork0.1802 50072 --
obs0.1823 52072 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.05 Å2 / Biso mean: 39.6611 Å2 / Biso min: 19.75 Å2
Refinement stepCycle: final / Resolution: 1.9→44.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 232 568 6231
Biso mean--44.23 47.2 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065830
X-RAY DIFFRACTIONf_angle_d0.8477865
X-RAY DIFFRACTIONf_chiral_restr0.047817
X-RAY DIFFRACTIONf_plane_restr0.0051026
X-RAY DIFFRACTIONf_dihedral_angle_d6.0994690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94750.35821430.3172357299
1.9475-2.00020.34431390.2673486100
2.0002-2.0590.2881420.23923552100
2.059-2.12550.29881410.22543528100
2.1255-2.20150.28451410.21473549100
2.2015-2.28960.2711430.20693557100
2.2896-2.39380.27611430.19513569100
2.3938-2.520.2781400.1977352799
2.52-2.67790.26321410.1877352999
2.6779-2.88460.25861430.1841358099
2.8846-3.17480.25211440.17983589100
3.1748-3.6340.22821430.1518359299
3.634-4.57770.17611470.14366899
4.5777-44.3440.19171500.1794377498

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