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- PDB-6yrc: Spectroscopically-validated structure of DtpB from Streptomyces l... -

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Basic information

Entry
Database: PDB / ID: 6yrc
TitleSpectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state
ComponentsPutative iron-dependent peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / dye-decolourising / spectroscopically-validated / ferric
Function / homology
Function and homology information


peroxidase activity / heme binding
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
Chem-7PE / PROTOPORPHYRIN IX CONTAINING FE / Putative iron-dependent peroxidase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLucic, M. / Dworkowski, F.S.N. / Worrall, J.A.R. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation.
Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / ...Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / Hough, M.A. / Worrall, J.A.R.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Revision 1.2May 1, 2024Group: 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
Revision 1.3Feb 11, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative iron-dependent peroxidase
B: Putative iron-dependent peroxidase
C: Putative iron-dependent peroxidase
D: Putative iron-dependent peroxidase
E: Putative iron-dependent peroxidase
F: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,78636
Polymers205,0336
Non-polymers7,75330
Water20,5731142
1
A: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4827
Polymers34,1721
Non-polymers1,3106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5946
Polymers34,1721
Non-polymers1,4215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0896
Polymers34,1721
Non-polymers9175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0993
Polymers34,1721
Non-polymers9272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8133
Polymers34,1721
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,70911
Polymers34,1721
Non-polymers2,53710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.790, 120.270, 196.010
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, 6 molecules ABCDEF

#1: Protein
Putative iron-dependent peroxidase


Mass: 34172.223 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SAMN05428941_7146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H2DDB9

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Non-polymers , 5 types, 1172 molecules

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


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H30O7
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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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Details

Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.12 % / Description: microcrystals
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: 6-10 mg/mL of protein in 50mM Sodium acteate, 150mM NaCl pH 5 mixed with 100 mM MgCl2, 100 mM HEPES pH 7.5, 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.99→49.05 Å / Num. obs: 138089 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.227 / Net I/σ(I): 7.5
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 5 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 32880 / CC1/2: 0.498 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SFX structure of ferric DtpB

Resolution: 1.99→49.05 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.198 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 6824 4.9 %RANDOM
Rwork0.1761 ---
obs0.1782 131265 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.89 Å2 / Biso mean: 30.279 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.99→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13912 0 375 1142 15429
Biso mean--34.82 37.53 -
Num. residues----1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01314770
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713497
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.67720132
X-RAY DIFFRACTIONr_angle_other_deg1.351.59231075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.32251864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.47220.781794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44152185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.60215135
X-RAY DIFFRACTIONr_chiral_restr0.070.21859
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217035
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023374
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 450 -
Rwork0.223 9454 -
all-9904 -
obs--96.69 %

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