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- PDB-7qzf: SFX structure of dye-type peroxidase DtpB D152A/N245A variant in ... -

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Basic information

Entry
Database: PDB / ID: 7qzf
TitleSFX structure of dye-type peroxidase DtpB D152A/N245A variant in the ferric state
ComponentsDyp-type peroxidase family
KeywordsOXIDOREDUCTASE / haem / peroxidase / ferric
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion 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
PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Shilova, A. / Owen, R.L. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R021015/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2022
Title: Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB.
Authors: Lucic, M. / Wilson, M.T. / Tosha, T. / Sugimoto, H. / Shilova, A. / Axford, D. / Owen, R.L. / Hough, M.A. / Worrall, J.A.R.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Dyp-type peroxidase family
F: Dyp-type peroxidase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,23413
Polymers204,5116
Non-polymers3,7237
Water12,376687
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23100 Å2
ΔGint-244 kcal/mol
Surface area68250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.950, 121.830, 199.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA7 - 3127 - 312
21GLUGLULEULEUBB7 - 3127 - 312
12GLUGLULEULEUAA7 - 3127 - 312
22GLUGLULEULEUCC7 - 3127 - 312
13PROPROGLUGLUAA8 - 3108 - 310
23PROPROGLUGLUDD8 - 3108 - 310
14GLUGLULEULEUAA7 - 3127 - 312
24GLUGLULEULEUEE7 - 3127 - 312
15GLUGLUASPASPAA7 - 3117 - 311
25GLUGLUASPASPFF7 - 3117 - 311
16GLUGLULEULEUBB7 - 3127 - 312
26GLUGLULEULEUCC7 - 3127 - 312
17PROPROGLUGLUBB8 - 3108 - 310
27PROPROGLUGLUDD8 - 3108 - 310
18GLUGLULEULEUBB7 - 3127 - 312
28GLUGLULEULEUEE7 - 3127 - 312
19GLUGLUASPASPBB7 - 3117 - 311
29GLUGLUASPASPFF7 - 3117 - 311
110PROPROGLUGLUCC8 - 3108 - 310
210PROPROGLUGLUDD8 - 3108 - 310
111GLUGLULEULEUCC7 - 3127 - 312
211GLUGLULEULEUEE7 - 3127 - 312
112GLUGLUASPASPCC7 - 3117 - 311
212GLUGLUASPASPFF7 - 3117 - 311
113PROPROGLUGLUDD8 - 3108 - 310
213PROPROGLUGLUEE8 - 3108 - 310
114PROPROGLUGLUDD8 - 3108 - 310
214PROPROGLUGLUFF8 - 3108 - 310
115GLUGLUASPASPEE7 - 3117 - 311
215GLUGLUASPASPFF7 - 3117 - 311

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Dyp-type peroxidase family /


Mass: 34085.191 Da / Num. of mol.: 6 / Mutation: D152A, N245A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SSPG_00656 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U8UU09
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: 6.2 mg/mL of protein in 20mM Sodium phosphate buffer, 150mM NaCl pH 7 mixed with 125 mM mM MgCl2, 125 mM HEPES pH 7.5, 18% PEG 4000

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Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.127 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 11, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.2→32.1 Å / Num. obs: 108174 / % possible obs: 100 % / Redundancy: 1040 % / CC1/2: 0.926 / R split: 0.219 / Net I/σ(I): 3.88
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 10679 / CC1/2: 0.509 / R split: 1.088

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFEL0.10.0data reduction
CrystFEL0.10.0data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRJ

6yrj


Resolution: 2.2→32.1 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.85 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 5434 5 %RANDOM
Rwork0.2181 ---
obs0.2206 102375 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.21 Å2 / Biso mean: 32.316 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2---1.4 Å20 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 2.2→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13889 0 259 687 14835
Biso mean--26.81 36.23 -
Num. residues----1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01314626
X-RAY DIFFRACTIONr_bond_other_d0.0010.01413478
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.67719971
X-RAY DIFFRACTIONr_angle_other_deg1.3881.59230948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12251855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71520.508788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.214152182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.14215139
X-RAY DIFFRACTIONr_chiral_restr0.0870.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216873
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023459
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88510.09
12B88510.09
21A88810.09
22C88810.09
31A88670.08
32D88670.08
41A88370.08
42E88370.08
51A88140.09
52F88140.09
61B88840.08
62C88840.08
71B88270.07
72D88270.07
81B88840.08
82E88840.08
91B88650.08
92F88650.08
101C88600.08
102D88600.08
111C88910.08
112E88910.08
121C89200.08
122F89200.08
131D87960.07
132E87960.07
141D87920.08
142F87920.08
151E88720.08
152F88720.08
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 406 -
Rwork0.321 7478 -
all-7884 -
obs--100 %

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