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- PDB-6kmm: Crystal Structure of HEPES bound Dye Decolorizing peroxidase from... -

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Basic information

Entry
Database: PDB / ID: 6kmm
TitleCrystal Structure of HEPES bound Dye Decolorizing peroxidase from Bacillus subtilis
ComponentsDeferrochelatase/peroxidase EfeB
KeywordsOXIDOREDUCTASE / Dye-decolorizing peroxidase / ferredoxin like fold / HEPES
Function / homology
Function and homology information


protoporphyrin ferrochelatase / iron import into cell / ferrochelatase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol
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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / PHOSPHATE ION / : / Deferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDhankhar, P. / Dalal, V. / Mahto, J.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT-1088-BIO India
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Characterization of dye-decolorizing peroxidase from Bacillus subtilis.
Authors: Dhankhar, P. / Dalal, V. / Mahto, J.K. / Gurjar, B.R. / Tomar, S. / Sharma, A.K. / Kumar, P.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase/peroxidase EfeB
B: Deferrochelatase/peroxidase EfeB
C: Deferrochelatase/peroxidase EfeB
D: Deferrochelatase/peroxidase EfeB
E: Deferrochelatase/peroxidase EfeB
F: Deferrochelatase/peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,59036
Polymers241,4126
Non-polymers6,17830
Water37,7592096
1
A: Deferrochelatase/peroxidase EfeB
hetero molecules

E: Deferrochelatase/peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,46612
Polymers80,4712
Non-polymers1,99610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area9210 Å2
ΔGint-50 kcal/mol
Surface area28700 Å2
MethodPISA
2
B: Deferrochelatase/peroxidase EfeB
C: Deferrochelatase/peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,48813
Polymers80,4712
Non-polymers2,01711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-102 kcal/mol
Surface area28400 Å2
MethodPISA
3
D: Deferrochelatase/peroxidase EfeB
hetero molecules

F: Deferrochelatase/peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63611
Polymers80,4712
Non-polymers2,1669
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area8530 Å2
ΔGint-74 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.837, 101.905, 105.405
Angle α, β, γ (deg.)88.000, 76.430, 83.280
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Deferrochelatase/peroxidase EfeB


Mass: 40235.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: efeB, FC605_19685 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P9FDJ4, UniProt: P39597*PLUS

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Non-polymers , 9 types, 2126 molecules

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


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2096 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 26% MPD, 0.05 M HEPES

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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: Sep 28, 2018
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.93→69.91 Å / Num. obs: 223932 / % possible obs: 92.8 % / Redundancy: 6.5 % / CC1/2: 0.99 / Net I/σ(I): 9.6
Reflection shellResolution: 1.93→1.96 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10799 / CC1/2: 0.95 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRC

4grc


Resolution: 1.93→69.91 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.32 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 11128 5 %RANDOM
Rwork0.1605 ---
obs0.1626 212663 92.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.16 Å2 / Biso mean: 45.601 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.81 Å2-0.74 Å2
2--0.62 Å2-2.28 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 1.93→69.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16818 0 413 2096 19327
Biso mean--49.7 54.44 -
Num. residues----2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01217767
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.67424043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37152189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94423.86873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.339153035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591574
X-RAY DIFFRACTIONr_chiral_restr0.1170.22236
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213610
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 827 -
Rwork0.312 15407 -
all-16234 -
obs--90.89 %
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)
11.081-0.18220.01931.4410.34130.8174-0.02640.14920.0469-0.17860.0649-0.0713-0.03850.1203-0.03850.0584-0.0381-0.00680.0916-0.03690.0687-0.34720.29760.8069
20.88020.22750.38220.7880.00630.96410.1117-0.0342-0.20620.0597-0.0356-0.02630.23340.0445-0.07610.06190.0126-0.0270.0814-0.0760.145132.440742.297541.4489
30.82670.01030.33980.7117-0.15111.0534-0.05650.06590.1074-0.06550.01250.1538-0.10160.01670.0440.0241-0.0012-0.03450.0758-0.06180.131321.631567.416924.7334
41.22550.17250.10020.4432-0.12551.2666-0.0685-0.15120.04480.1079-0.0478-0.0024-0.09560.01680.11630.0585-0.0045-0.03270.0438-0.02160.065339.488472.42-15.2933
50.9416-0.13410.09640.93750.33350.7194-0.0831-0.09960.23150.0008-0.03580.1576-0.1369-0.12440.11890.06590.0095-0.04350.0827-0.08920.19660.39420.274917.3168
60.95160.05780.05590.605-0.0451.0892-0.10260.3190.1661-0.0226-0.0509-0.1148-0.17230.26410.15340.055-0.0855-0.05790.20520.09530.1288-3.335881.622658.7885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 363
2X-RAY DIFFRACTION1A401 - 406
3X-RAY DIFFRACTION1A501 - 552
4X-RAY DIFFRACTION2B2 - 362
5X-RAY DIFFRACTION2B401 - 404
6X-RAY DIFFRACTION2B501 - 700
7X-RAY DIFFRACTION3C2 - 362
8X-RAY DIFFRACTION3C401 - 407
9X-RAY DIFFRACTION3C501 - 651
10X-RAY DIFFRACTION4D2 - 363
11X-RAY DIFFRACTION4D401 - 406
12X-RAY DIFFRACTION4D501 - 751
13X-RAY DIFFRACTION5E3 - 362
14X-RAY DIFFRACTION5E401 - 404
15X-RAY DIFFRACTION5E501 - 713
16X-RAY DIFFRACTION6F1 - 363
17X-RAY DIFFRACTION6F401 - 403

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