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- PDB-6gzw: Ferric DtpA from Streptomyces lividans -

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Basic information

Entry
Database: PDB / ID: 6gzw
TitleFerric DtpA from Streptomyces lividans
ComponentsDye type peroxidase A
KeywordsOXIDOREDUCTASE / peroxidase / ferric / dye-type
Function / homology
Function and homology information


iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Deferrochelatase / 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
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMoreno Chicano, T. / Worrall, J.A.R. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2014-355 United Kingdom
CitationJournal: Chemistry / Year: 2019
Title: An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis.
Authors: Chaplin, A.K. / Chicano, T.M. / Hampshire, B.V. / Wilson, M.T. / Hough, M.A. / Svistunenko, D.A. / Worrall, J.A.R.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Dye type peroxidase A
B: Dye type peroxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3964
Polymers81,1632
Non-polymers1,2332
Water14,286793
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-54 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.118, 71.032, 78.089
Angle α, β, γ (deg.)90.000, 92.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dye type peroxidase A / Dye type peroxidase A from Streptomyces lividans


Mass: 40581.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Plasmid: pet28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A076MAJ9
#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.: 793 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystals were grown by the vapour diffusion hanging drop method using a ferric protein solution at 13 mg/ml equilibrated against a reservoir consisting of 17-24% PEG 3000 and 50-100 mM sodium citrate, pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.41→77.99 Å / Num. obs: 118339 / % possible obs: 93.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.06 / Rrim(I) all: 0.141 / Net I/σ(I): 7.8
Reflection shellResolution: 1.41→1.46 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.253 / Num. unique obs: 9905 / CC1/2: 0.529 / Rpim(I) all: 0.593 / Rrim(I) all: 1.391 / % possible all: 80.4

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
EDNAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAP

5map


Resolution: 1.41→77.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.757 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0768 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 5945 5 %RANDOM
Rwork0.1891 ---
obs0.1905 112316 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 48.47 Å2 / Biso mean: 15.64 Å2 / Biso min: 3.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.17 Å2
2--0.74 Å20 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 1.41→77.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5619 0 86 793 6498
Biso mean--10.39 23.18 -
Num. residues----740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195952
X-RAY DIFFRACTIONr_bond_other_d0.0020.025416
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9728099
X-RAY DIFFRACTIONr_angle_other_deg0.983312487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42222.465284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10315916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6621571
X-RAY DIFFRACTIONr_chiral_restr0.0910.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216936
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021343
LS refinement shellResolution: 1.41→1.447 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 363 -
Rwork0.323 6709 -
all-7072 -
obs--76.03 %

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