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- PDB-6tb8: Dye Type Peroxidase Aa from Streptomyces lividans: spectroscopica... -

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Basic information

Entry
Database: PDB / ID: 6tb8
TitleDye Type Peroxidase Aa from Streptomyces lividans: spectroscopically-validated ferric state
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / metalloprotein / iron / dye type
Function / homology
Function and homology information


iron import into cell / ferrochelatase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
Deferrochelatase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Deferrochelatase/peroxidase / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLucic, M. / Moreno-Chicano, T.M. / Hough, M.A. / Dworkowski, F.S.N. / Worrall, J.A.R.
CitationJournal: Dalton Trans / Year: 2020
Title: A subtle structural change in the distal haem pocket has a remarkable effect on tuning hydrogen peroxide reactivity in dye decolourising peroxidases from Streptomyces lividans.
Authors: Lucic, M. / Chaplin, A.K. / Moreno-Chicano, T. / Dworkowski, F.S.N. / Wilson, M.T. / Svistunenko, D.A. / Hough, M.A. / Worrall, J.A.R.
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,7454
Polymers80,5122
Non-polymers1,2332
Water15,277848
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-60 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.400, 67.590, 72.900
Angle α, β, γ (deg.)90.000, 105.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase/peroxidase


Mass: 40256.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLIV_26340 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A076MF68, UniProt: Q9RKQ2*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7
Details: 1:1 RATIO OF A 6.5 MG/ML DTPAA PROTEIN SOLUTION WITH A PRECIPITANT SOLUTION CONTAINING 20% PEG 6000, 100 MM HEPES PH 7.0, BATCH MODE, TEMPERATURE 291K

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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: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.8→48.71 Å / Num. obs: 61725 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.089 / Rrim(I) all: 0.198 / Net I/av σ(I): 6.3 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3542 / CC1/2: 0.683 / Rpim(I) all: 0.365 / Rrim(I) all: 0.682 / % possible all: 96.1

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I43

6i43


Resolution: 1.8→43.679 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.1991 2990 4.85 %
Rwork0.1513 --
obs0.1537 61692 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.53 Å2 / Biso mean: 20.281 Å2 / Biso min: 6.81 Å2
Refinement stepCycle: final / Resolution: 1.8→43.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 86 848 6427
Biso mean--13.07 27.52 -
Num. residues----724
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82950.31711180.2494271695
1.8295-1.86110.28991270.2375276699
1.8611-1.89490.26781540.21082775100
1.8949-1.93140.2451380.21262829100
1.9314-1.97080.26311270.1975279899
1.9708-2.01370.27081470.18752772100
2.0137-2.06050.26351440.1755275199
2.0605-2.1120.21751350.17432799100
2.112-2.16910.21431290.1592816100
2.1691-2.2330.2211310.15792810100
2.233-2.3050.20331270.1552825100
2.305-2.38740.22921400.1562798100
2.3874-2.4830.21141410.15482792100
2.483-2.5960.21691330.14862829100
2.596-2.73280.20341550.143278399
2.7328-2.9040.20221560.1452804100
2.904-3.12820.1861420.14122800100
3.1282-3.44290.19991740.13282792100
3.4429-3.94080.15971510.1186282399
3.9408-4.96390.12551510.1106279599
4.9639-43.6790.17381700.1468282998

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