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- PDB-6i43: SFX Structure of Damage Free Ferric State of Dye Type Peroxidase ... -

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Basic information

Entry
Database: PDB / ID: 6i43
TitleSFX Structure of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces lividans
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / peroxidase
Function / homology
Function and homology information


ferrochelatase activity / iron import into cell / cell envelope / 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
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsEbrahim, A. / Moreno-Chicano, T. / Chaplin, A.K. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R.
CitationJournal: Iucrj / Year: 2019
Title: Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins.
Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J.H. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. / ...Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J.H. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. / Axford, D. / Owen, R.L. / Hough, M.A.
History
DepositionNov 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: 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

Downloads & links

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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
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-61 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 68.180, 74.620
Angle α, β, γ (deg.)90.00, 105.58, 90.00
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
Details: ...Details: DPAGADAGSAVPFHGAHQAGIATPVQDRLHFAAFDVTTEDRAAFVALLKEWTAAARRLTAGHAVGEGAYGGLPEAPPDDTGEALGLKPSRLTLTIGFGPSLFTRFGLADLRPEALADLPKFPGDNLDRARSGGDLCVQACADDPQVAVHAIRNLARIGFGKVVVRWSQLGFGKTSSTTPDKQTPRNLLGFKDGTRNIAGTEKDRLDRFVWAAEKDGTPWMTGGSYLVARRIRMHIETWDRASLQEQEDVFGRDKGEGAPVGKAKERDEPFLKAMKPDAHVRLAHPDSNGGATLLRRGYSFTDGTDGLGRLDAGLFFLAYQRDIRTGFVPVQRNLATDALNEYIQHVGSAVFAVPPGVRDADDWWGSTLFGKEA
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: SCO2276 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9RKQ2, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.27 Å3/Da / Density % sol: 45.79 % / Description: Microcrystals
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

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Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.88→41.46 Å / Num. obs: 57351 / % possible obs: 100 % / Redundancy: 381 % / CC1/2: 0.993 / R split: 0.0722 / Net I/σ(I): 9.6
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 212 % / Mean I/σ(I) obs: 1.73 / CC1/2: 0.722 / R split: 0.583 / % possible all: 100
Serial crystallography measurementCollection time total: 240 hours / Focal spot size: 1.66 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / Pulse photon energy: 10.01 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Silicon nitride fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Mylar film / Sample solvent: Mother liquor

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5MAP

5map


Resolution: 1.88→35.458 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1665 2852 4.98 %
Rwork0.1319 --
obs0.1336 57312 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→35.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 86 362 5914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095718
X-RAY DIFFRACTIONf_angle_d0.9197801
X-RAY DIFFRACTIONf_dihedral_angle_d13.083301
X-RAY DIFFRACTIONf_chiral_restr0.052822
X-RAY DIFFRACTIONf_plane_restr0.0071035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.91240.35151350.32072736X-RAY DIFFRACTION100
1.9124-1.94720.26431550.23962673X-RAY DIFFRACTION100
1.9472-1.98460.21131620.18122686X-RAY DIFFRACTION100
1.9846-2.02510.23711480.17882730X-RAY DIFFRACTION100
2.0251-2.06920.19971450.17032696X-RAY DIFFRACTION100
2.0692-2.11730.21041270.15762725X-RAY DIFFRACTION100
2.1173-2.17020.17341580.13752674X-RAY DIFFRACTION100
2.1702-2.22890.19191290.13212710X-RAY DIFFRACTION100
2.2289-2.29450.17411370.13722743X-RAY DIFFRACTION100
2.2945-2.36850.20011300.13462702X-RAY DIFFRACTION100
2.3685-2.45320.17631350.14112722X-RAY DIFFRACTION100
2.4532-2.55140.20171440.14012734X-RAY DIFFRACTION100
2.5514-2.66740.17211410.14482726X-RAY DIFFRACTION100
2.6674-2.8080.17871350.14182736X-RAY DIFFRACTION100
2.808-2.98390.19141400.14142713X-RAY DIFFRACTION100
2.9839-3.21410.21380.13892738X-RAY DIFFRACTION100
3.2141-3.53730.161520.12182719X-RAY DIFFRACTION100
3.5373-4.04850.1251580.10282734X-RAY DIFFRACTION100
4.0485-5.09830.12841440.09692742X-RAY DIFFRACTION100
5.0983-35.4640.13531390.12892821X-RAY DIFFRACTION100

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