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- PDB-6i7c: Dye type peroxidase Aa from Streptomyces lividans: imidazole complex -

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Basic information

Entry
Database: PDB / ID: 6i7c
TitleDye type peroxidase Aa from Streptomyces lividans: imidazole complex
ComponentsDeferrochelatase/peroxidase
KeywordsOXIDOREDUCTASE / imidazole / 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 / IMIDAZOLE / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMoreno-Chicano, T. / Ebrahim, A. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Duyvesteyn, H.
CitationJournal: Iucrj / Year: 2019
Title: High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.
Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / ...Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / Tono, K. / Worrall, J.A.R. / Owen, R.L. / Hough, M.A.
History
DepositionNov 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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
Revision 1.3Jan 15, 2025Group: Structure summary / Category: audit_author / pdbx_entry_details / Item: _audit_author.name

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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)80,0576
Polymers78,6862
Non-polymers1,3714
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-51 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.480, 68.030, 73.530
Angle α, β, γ (deg.)90.000, 105.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase/peroxidase


Mass: 39343.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO2276 / Production host: Escherichia coli (E. coli)
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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7
Details: 1:1 ratio of a 6.5 mg/ml DtpAa protein solution with 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 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.88→37 Å / Num. obs: 56220 / % possible obs: 100 % / Redundancy: 102 % / CC1/2: 0.96 / R split: 0.158 / Rmerge(I) obs: 0.224 / Net I/σ(I): 5.7
Reflection shellResolution: 1.88→1.93 Å / Mean I/σ(I) obs: 1.54 / CC1/2: 0.6 / R split: 0.639 / % possible all: 100
Serial crystallography measurementCollection time total: 80 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 chip / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Mylar film / Sample solvent: Mother liquor

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5map

5map


Resolution: 1.88→35.295 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.45
Details: Data file deposited extends to higher resolution. The resolution limit was set in refinement
RfactorNum. reflection% reflection
Rfree0.1766 2830 5.04 %
Rwork0.1385 --
obs0.1404 56150 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.62 Å2 / Biso mean: 30.8175 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 1.88→35.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 165 414 6046
Biso mean--24.5 34.38 -
Num. residues----725
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.88-1.91240.29621380.289726442782
1.9124-1.94720.29531420.212126422784
1.9472-1.98460.2281540.186626452799
1.9846-2.02510.22381220.180926662788
2.0251-2.06920.22361410.171926602801
2.0692-2.11730.20261650.15526152780
2.1173-2.17020.20261470.1426532800
2.1702-2.22890.19481290.13326652794
2.2289-2.29450.17771430.138226442787
2.2945-2.36850.18221260.135926932819
2.3685-2.45320.17521320.135926702802
2.4532-2.55140.18031520.133626342786
2.5514-2.66740.21261370.138726662803
2.6674-2.8080.16841320.138926792811
2.808-2.98390.19121490.139926512800
2.9839-3.21410.18431520.141226832835
3.2141-3.53730.15431640.131126512815
3.5373-4.04850.16241230.111226982821
4.0485-5.09820.13441370.112726992836
5.0982-35.30090.15431450.151227622907

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