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- PDB-4grc: Crystal structure of DyP-type peroxidase (SCO2276) from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 4grc
TitleCrystal structure of DyP-type peroxidase (SCO2276) from Streptomyces coelicolor
ComponentsPutative membrane protein
KeywordsOXIDOREDUCTASE / ferridoxin-like
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 / HYDROGEN PEROXIDE / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLukk, T. / Hetta, A.M.A. / Jones, A. / Solbiati, J. / Majumdar, S. / Cronan, J.E. / Gerlt, J.A. / Nair, S.K.
CitationJournal: To be Published
Title: DyP-type peroxidases from Stretptomyces and Thermobifida can modify organosolv lignin.
Authors: Lukk, T. / Hetta, A.M.A. / Jones, A. / Solbiati, J. / Majumdar, S. / Cronan, J.E. / Gerlt, J.A. / Nair, S.K.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4414
Polymers46,7501
Non-polymers6913
Water6,972387
1
A: Putative membrane protein
hetero molecules

A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8818
Polymers93,5002
Non-polymers1,3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7050 Å2
ΔGint-61 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.990, 71.990, 170.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-987-

HOH

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Components

#1: Protein Putative membrane protein / / Dyp-type peroxidase


Mass: 46750.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO2276 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RKQ2, dye decolorizing peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: Mother liqueur contained 0.2M CaCl2, 0.1M Hepes (pH 7.5) and 28% PEG400. Protein concentration was 15 mg/mL in a buffer containing 100 mM KCl and 50 mM Hepes 8.0. 0.5 uL protein was mixed ...Details: Mother liqueur contained 0.2M CaCl2, 0.1M Hepes (pH 7.5) and 28% PEG400. Protein concentration was 15 mg/mL in a buffer containing 100 mM KCl and 50 mM Hepes 8.0. 0.5 uL protein was mixed with equal volume of mother liqueur, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 22, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionNumber: 643289 / Rmerge(I) obs: 0.095 / D res high: 2 Å / Num. obs: 66865 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.943071896.810.03
6.328.94138810010.033
5.166.32173910010.038
4.475.16212410010.037
44.47235410010.041
3.654264310010.047
3.383.65287810010.052
3.163.38306910010.068
2.983.16325110010.084
2.832.98349910010.104
2.72.83362410010.123
2.582.7377610010.153
2.482.58395910010.189
2.392.48413710010.223
2.312.39427510010.269
2.242.31442810010.323
2.172.24454210010.386
2.112.17468610010.442
2.052.11481510010.509
22.05496010010.675
ReflectionResolution: 2→30 Å / Num. obs: 35482 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 23.97 Å2 / Rsym value: 0.095 / Net I/σ(I): 19.09
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2-2.054.2849600.6751100
2.05-2.115.4348150.5091100
2.11-2.176.246860.4421100
2.17-2.247.145420.3861100
2.24-2.318.1844280.3231100
2.31-2.399.3842750.2691100
2.39-2.4811.0941370.2231100
2.48-2.5812.5839590.1891100
2.58-2.715.3237760.1531100
2.7-2.8317.8536240.1231100
2.83-2.9821.0834990.1041100
2.98-3.1625.3532510.0841100
3.16-3.3830.8330690.0681100
3.38-3.6537.4828780.0521100
3.65-442.0126430.0471100
4-4.4745.7323540.0411100
4.47-5.1648.2721240.0371100
5.16-6.3247.3217390.0381100
6.32-8.9451.6213880.0331100
8.94-3054.977180.03196.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1066refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GVK

2gvk


Resolution: 2→29.283 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8894 / SU ML: 0.17 / Cross valid method: thorough / σ(F): 2.02 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1774 5 %random
Rwork0.1594 ---
obs0.1613 35482 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.93 Å2 / Biso mean: 24.2439 Å2 / Biso min: 4.59 Å2
Refinement stepCycle: LAST / Resolution: 2→29.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 46 387 3171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072888
X-RAY DIFFRACTIONf_angle_d1.013935
X-RAY DIFFRACTIONf_chiral_restr0.073408
X-RAY DIFFRACTIONf_plane_restr0.004525
X-RAY DIFFRACTIONf_dihedral_angle_d14.331037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.05420.24671350.189325512686
2.0542-2.11460.20751350.175425662701
2.1146-2.18280.19441330.163625262659
2.1828-2.26080.19711340.154525652699
2.2608-2.35130.21941350.155525602695
2.3513-2.45830.22971350.156525572692
2.4583-2.58780.20661350.165125632698
2.5878-2.74980.21061360.158925932729
2.7498-2.96190.20991350.16725712706
2.9619-3.25970.23641370.171325982735
3.2597-3.73050.17851380.156326172755
3.7305-4.69690.17331390.135126512790
4.6969-29.28610.17431470.166427902937

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