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- PDB-4gu7: Crystal structure of DyP-type peroxidase (SCO7193) from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 4gu7
TitleCrystal structure of DyP-type peroxidase (SCO7193) from Streptomyces coelicolor
ComponentsPutative uncharacterized protein SCO7193
KeywordsOXIDOREDUCTASE / ferridoxin-like
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / reflns_shell
Item: _pdbx_diffrn_reflns_shell.percent_possible_obs / _reflns_shell.percent_possible_all
Revision 1.2Sep 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein SCO7193
B: Putative uncharacterized protein SCO7193
C: Putative uncharacterized protein SCO7193
D: Putative uncharacterized protein SCO7193
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,9399
Polymers145,4144
Non-polymers2,5255
Water0
1
A: Putative uncharacterized protein SCO7193
D: Putative uncharacterized protein SCO7193
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9995
Polymers72,7072
Non-polymers1,2923
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-68 kcal/mol
Surface area24820 Å2
MethodPISA
2
B: Putative uncharacterized protein SCO7193
C: Putative uncharacterized protein SCO7193
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9404
Polymers72,7072
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-60 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.950, 188.950, 188.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
Putative uncharacterized protein SCO7193 / DyP-type peroxidase


Mass: 36353.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO7193 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FBY9, dye decolorizing peroxidase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein solution was at 15 mg/mL, containing 20 mM HEPES and 100 mM KCl. Mother liqueur contained 2.0 M (NH4)2SO4. Cryoprotectant contained 25% glycerol, pH 8.0, vapor diffusion, hanging drop, temperature 277K

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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 10, 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: 1282277 / Rmerge(I) obs: 0.161 / D res high: 3.1 Å / Num. obs: 78789 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
13.86205916610.049
9.813.86162310010.042
89.8209710010.048
6.938247310010.065
6.26.93279210010.085
5.666.2314110010.096
5.245.66335210010.104
4.95.24368710010.097
4.624.9381699.710.095
4.384.62408710010.102
4.184.38432010010.125
44.18453710010.144
3.854467210010.175
3.713.85479510010.214
3.583.71511010010.261
3.473.58520810010.323
3.363.47540410010.393
3.273.36552710010.498
3.183.27566910010.639
3.13.18588810010.827
ReflectionResolution: 3.1→20 Å / Num. obs: 40721 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.645 Å2 / Rsym value: 0.161 / Net I/σ(I): 19.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.1-3.180.8274.249489058881100
3.18-3.270.6395.459167456691100
3.27-3.360.4986.988974455271100
3.36-3.470.3938.778788654041100
3.47-3.580.32310.498476352081100
3.58-3.710.26112.848324851101100
3.71-3.850.21415.237822047951100
3.85-40.17518.17619146721100
4-4.180.14421.257404045371100
4.18-4.380.12523.737054543201100
4.38-4.620.10228.186677540871100
4.62-4.90.09529.26623543816199.7
4.9-5.240.09729.456025136871100
5.24-5.660.10427.645488733521100
5.66-6.20.09629.685139131411100
6.2-6.930.08532.684565627921100
6.93-80.06540.224041524731100
8-9.80.04851.893410620971100
9.8-13.860.04257.212611616231100
13.86-200.04952.099125591166

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GVK

2gvk


Resolution: 3.1→19.489 Å / Occupancy max: 1 / Occupancy min: 0.59 / FOM work R set: 0.8688 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2036 5 %random
Rwork0.157 ---
all0.226 40724 --
obs0.1594 40721 99.99 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.509 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 111.05 Å2 / Biso mean: 49.8198 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9452 0 173 0 9625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099860
X-RAY DIFFRACTIONf_angle_d1.27613460
X-RAY DIFFRACTIONf_chiral_restr0.0721464
X-RAY DIFFRACTIONf_plane_restr0.0071788
X-RAY DIFFRACTIONf_dihedral_angle_d14.4183544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.17310.32691330.249525272660100
3.1731-3.25210.31431350.230425662701100
3.2521-3.33960.29371340.20925502684100
3.3396-3.43740.25071350.21125662701100
3.4374-3.54770.24511340.1791254826821.01
3.5477-3.67370.21771350.172525642699100
3.6737-3.81970.23531350.161525662701100
3.8197-3.99220.21111360.150425882724100
3.9922-4.20070.18341350.138725552690100
4.2007-4.46090.17261350.130125612696100
4.4609-4.80060.14211360.1122258827241.01
4.8006-5.27490.14971370.134625952732100
5.2749-6.01850.19461360.153526022738100
6.0185-7.50980.19531380.158326112749100
7.5098-19.48910.17271420.133326982840100

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