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- PDB-7zmj: SFX structure of dye-type peroxidase DtpB R243A variant in the fe... -

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Basic information

Entry
Database: PDB / ID: 7zmj
TitleSFX structure of dye-type peroxidase DtpB R243A variant in the ferric state
ComponentsPutative dye-decolorizing peroxidase (DyP), encapsulated subgroup
KeywordsOXIDOREDUCTASE / haem / peroxidase / ferric
Function / homologyDyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / peroxidase activity / heme binding / PROTOPORPHYRIN IX CONTAINING FE / Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
Function and homology information
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLucic, M. / Worrall, J.A.R. / Hough, M.A. / Shilova, A. / Axford, D.A. / Owen, R.L. / 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
DepositionApr 19, 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: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
B: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
C: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
D: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
E: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
F: Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,69614
Polymers198,9486
Non-polymers3,7488
Water15,601866
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22410 Å2
ΔGint-236 kcal/mol
Surface area67630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.600, 121.300, 197.600
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 - 3121 - 306
21GLUGLULEULEUBB7 - 3121 - 306
12GLUGLULEULEUAA7 - 3121 - 306
22GLUGLULEULEUCC7 - 3121 - 306
13PROPROGLUGLUAA8 - 3102 - 304
23PROPROGLUGLUDD8 - 3102 - 304
14PROPROASPASPAA8 - 3112 - 305
24PROPROASPASPEE8 - 3112 - 305
15PROPROASPASPAA8 - 3112 - 305
25PROPROASPASPFF8 - 3112 - 305
16GLUGLULEULEUBB7 - 3121 - 306
26GLUGLULEULEUCC7 - 3121 - 306
17PROPROGLUGLUBB8 - 3102 - 304
27PROPROGLUGLUDD8 - 3102 - 304
18PROPROASPASPBB8 - 3112 - 305
28PROPROASPASPEE8 - 3112 - 305
19PROPROASPASPBB8 - 3112 - 305
29PROPROASPASPFF8 - 3112 - 305
110PROPROGLUGLUCC8 - 3102 - 304
210PROPROGLUGLUDD8 - 3102 - 304
111PROPROASPASPCC8 - 3112 - 305
211PROPROASPASPEE8 - 3112 - 305
112PROPROASPASPCC8 - 3112 - 305
212PROPROASPASPFF8 - 3112 - 305
113PROPROGLUGLUDD8 - 3102 - 304
213PROPROGLUGLUEE8 - 3102 - 304
114PROPROGLUGLUDD8 - 3102 - 304
214PROPROGLUGLUFF8 - 3102 - 304
115PROPROASPASPEE8 - 3112 - 305
215PROPROASPASPFF8 - 3112 - 305

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
Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup


Mass: 33158.062 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SLI_7409 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9HFU5
#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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: 6.2 mg/mL of protein in 20mM Sodium phosphate, 150mM NaCl pH 7 mixed with 125 mM MgCl2, 125 mM HEPES, 18% PEG 4000, pH 7.5

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Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.13 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 6, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2→35.27 Å / Num. obs: 140951 / % possible obs: 100 % / Redundancy: 207.8 % / CC1/2: 0.947 / R split: 0.194 / Net I/σ(I): 4.09
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 13959 / CC1/2: 0.48 / R split: 0.79
Serial crystallography measurementPulse duration: 10 fsec.
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: HEC / Filter size: 30 µm / Flow rate: 0.0068 µL/min / Injector diameter: 100 µm
Serial crystallography data reductionXFEL pulse events: 5000

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.10.0data reduction
CrystFEL0.10.0data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRJ

6yrj


Resolution: 2→35.27 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.759 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 6916 4.9 %RANDOM
Rwork0.2015 ---
obs0.2028 133981 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.05 Å2 / Biso mean: 28.357 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2--0.28 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 2→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13860 0 260 866 14986
Biso mean--22.01 34.96 -
Num. residues----1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01314691
X-RAY DIFFRACTIONr_bond_other_d0.0010.01413506
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.67720075
X-RAY DIFFRACTIONr_angle_other_deg1.3781.59331020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70251873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.22720.556792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.864152191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.03815139
X-RAY DIFFRACTIONr_chiral_restr0.0750.21862
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217021
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023487
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89420.08
12B89420.08
21A90560.08
22C90560.08
31A90170.07
32D90170.07
41A89280.08
42E89280.08
51A90100.07
52F90100.07
61B89810.08
62C89810.08
71B89650.07
72D89650.07
81B90920.05
82E90920.05
91B89410.07
92F89410.07
101C90550.07
102D90550.07
111C89530.08
112E89530.08
121C90850.07
122F90850.07
131D90400.08
132E90400.08
141D90920.07
142F90920.07
151E90410.07
152F90410.07
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 538 -
Rwork0.381 9783 -
all-10321 -
obs--100 %

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