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- PDB-4gt2: Crystal structure of DyP-type peroxidase (SCO3963) from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 4gt2
TitleCrystal structure of DyP-type peroxidase (SCO3963) from Streptomyces coelicolor
ComponentsPutative uncharacterized protein SCO3963
KeywordsOXIDOREDUCTASE / ferridoxin-like
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 / cytosol
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Deferrochelatase/peroxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 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_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_label_asym_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.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_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 / _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
B: Putative uncharacterized protein SCO3963
A: Putative uncharacterized protein SCO3963
E: Putative uncharacterized protein SCO3963
G: Putative uncharacterized protein SCO3963
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,40921
Polymers197,0194
Non-polymers3,39017
Water40,1552229
1
B: Putative uncharacterized protein SCO3963
A: Putative uncharacterized protein SCO3963
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23411
Polymers98,5102
Non-polymers1,7249
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-55 kcal/mol
Surface area27700 Å2
MethodPISA
2
E: Putative uncharacterized protein SCO3963
G: Putative uncharacterized protein SCO3963
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17510
Polymers98,5102
Non-polymers1,6658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-55 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.870, 203.200, 76.320
Angle α, β, γ (deg.)90.000, 110.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules BAEG

#1: Protein
Putative uncharacterized protein SCO3963 / DyP-type peroxidase


Mass: 49254.777 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: SCO3963 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZBW9, dye decolorizing peroxidase

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Non-polymers , 5 types, 2246 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2229 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
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 5% Tacsimate, 100 mM HEPES, 15% PEG 5,000 MME. Cryoprotectant contained 20% glycerol, pH 8. ...Details: Protein solution was at 15 mg/mL, containing 20 mM HEPES and 100 mM KCl. Mother liqueur contained 5% Tacsimate, 100 mM HEPES, 15% PEG 5,000 MME. Cryoprotectant contained 20% 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 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: 883353 / Rmerge(I) obs: 0.092 / D res high: 1.8 Å / Num. obs: 278491 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.0530302595.810.04
5.698.05572599.110.046
4.655.6973949910.045
4.024.65865298.910.047
3.64.02981498.610.049
3.293.61092198.610.054
3.043.291187498.610.062
2.853.041267298.810.071
2.682.851365098.910.082
2.552.68143179910.096
2.432.551521199.110.109
2.322.431584799.310.115
2.232.321644099.210.132
2.152.231718299.410.142
2.082.151784499.410.16
2.012.081844399.310.187
1.952.011906699.610.224
1.91.951967699.710.274
1.851.92018699.810.323
1.81.85205529910.372
Reflection twinOperator: h,-k,-h-l / Fraction: 0.01
ReflectionResolution: 1.8→30 Å / Num. all: 280892 / Num. obs: 141255 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.643 Å2 / Rsym value: 0.092 / Net I/σ(I): 10.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.3722.765614120552199
1.85-1.90.3233.56158320186199.8
1.9-1.950.2744.336308519676199.7
1.95-2.010.2245.196119019066199.6
2.01-2.080.1876.155924718443199.3
2.08-2.150.167.125740517844199.4
2.15-2.230.1427.995529117182199.4
2.23-2.320.1328.555312616440199.2
2.32-2.430.1159.655117315847199.3
2.43-2.550.10910.034922515211199.1
2.55-2.680.09611.54631314317199
2.68-2.850.08213.194404613650198.9
2.85-3.040.07114.914081312672198.8
3.04-3.290.06216.913819911874198.6
3.29-3.60.05419.383499710921198.6
3.6-4.020.04920.83315139814198.6
4.02-4.650.04721.85278018652198.9
4.65-5.690.04522.04239957394199
5.69-8.050.04621.04186785725199.1
8.05-300.0423.5595323025195.8

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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
Resolution: 1.8→29.2 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.9076 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 7154 5.06 %random
Rwork0.1474 ---
obs0.149 141255 99.74 %-
all-141791 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.59 Å2 / Biso mean: 15.8213 Å2 / Biso min: 0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11242 0 232 2229 13703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711826
X-RAY DIFFRACTIONf_angle_d1.10216048
X-RAY DIFFRACTIONf_chiral_restr0.0741631
X-RAY DIFFRACTIONf_plane_restr0.0052175
X-RAY DIFFRACTIONf_dihedral_angle_d14.1284328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83020.20283400.1716554689493
1.8302-1.86350.19813540.16426793714795
1.8635-1.89930.20183630.16466635699895
1.8993-1.93810.17543460.15626696704295
1.9381-1.98020.18823920.15716642703494
1.9802-2.02630.16643320.15056704703695
2.0263-2.07690.17763510.15416749710095
2.0769-2.1330.1813420.15026695703795
2.133-2.19580.18543650.15086691705695
2.1958-2.26660.19173620.15156691705395
2.2666-2.34750.19483620.15086752711495
2.3475-2.44150.19943390.15126701704095
2.4415-2.55250.20373370.15646778711595
2.5525-2.68690.20664200.15186577699794
2.6869-2.8550.20013860.14896707709395
2.855-3.07510.18733350.14386707704295
3.0751-3.38390.17243590.13476759711895
3.3839-3.8720.16683290.12396737706695
3.872-4.87240.1433750.11526727710295
4.8724-25.02060.21693650.17896758712395
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2186-0.2338-1.44010.06460.25561.6691-0.04610.0695-0.2022-0.02340.01160.10040.1761-0.09990.00540.12-0.0239-0.01270.1032-0.01260.1385-3.8438-44.909120.9045
20.51190.2143-0.1570.3144-0.04710.5876-0.01080.0236-0.06180.01190.0042-0.05370.07440.06970.00780.0620.0096-0.00320.0648-0.00880.085611.5406-38.502720.8204
30.3515-0.0563-0.00130.28-0.01370.4526-0.00030.0455-0.0123-0.0311-0.0003-0.01820.01410.03470.00150.0567-0.0059-0.00290.0674-0.0020.05994.9512-29.238812.9085
40.47710.04220.08680.40630.14260.7438-0.01190.03620.0265-0.0456-0.01570.0833-0.0549-0.09420.02870.0571-0.0008-0.00390.05620.0030.0542-15.2341-17.52035.4099
50.6043-0.2622-0.21460.57670.10290.6414-0.00820.03970.0425-0.02720.0047-0.034-0.06110.05350.00090.0523-0.0126-0.00090.05790.00110.05231.5118-18.373610.8398
62.45560.41990.22612.7759-1.01322.3399-0.06220.0372-0.317-0.07590.0384-0.15280.32810.13640.030.13740.02530.0170.0945-0.03380.129415.2996-46.116110.0762
70.26640.03620.08910.41890.17020.5196-0.0171-0.00320.01550.0054-0.00180.0419-0.0282-0.07730.02210.06260.0089-0.00180.06870.0030.0576-14.2456-16.752437.6548
80.3736-0.1020.09640.3105-0.04870.4113-0.0307-0.04820.02560.04570.0258-0.0181-0.0427-0.02780.00220.05890.0041-0.00380.0596-0.00690.0501-3.1884-19.533445.1938
90.3404-0.18830.05880.58620.18290.5311-0.0156-0.047-0.02580.10830.0409-0.06270.05990.0403-0.01340.07320.0047-0.01370.0691-0.00260.06388.8975-32.950750.5359
101.1736-0.40620.09690.780.04540.4211-0.0282-0.02230.01160.03040.00820.0283-0.0324-0.04580.00630.06030.0093-0.00850.054-0.01280.035-4.0732-15.767447.3599
110.03860.20740.21761.19271.30721.37940.02360.08150.1144-0.1117-0.05730.0875-0.0853-0.15920.0350.11880.0188-0.03040.13070.01680.1415-18.896628.6134.0866
120.2955-0.3163-0.10761.11920.01510.3428-0.017-0.0106-0.0512-0.07850.00010.01820.028-0.06130.01330.0865-0.0145-0.00990.08990.00650.0739-12.013911.86613.2699
130.3157-0.1655-0.15520.43730.33950.861-0.03450.0034-0.0456-0.02230.00050.07810.0496-0.06460.03550.0802-0.00420.00340.06360.00110.0848-13.900514.71037.9424
140.37320.0877-0.04790.18930.00260.4668-0.01010.0386-0.0063-0.05320.0038-0.01680.02090.00770.00770.08470.0012-0.00010.0695-0.00250.08-2.543619.6026-0.7164
150.84090.6518-0.03631.40710.41350.8411-0.03460.17490.0003-0.16550.05310.10360.0244-0.0579-0.01660.0964-0.01570.00050.09320.00350.0662-6.227316.6041-9.9164
161.15080.04790.19851.0215-0.29911.5494-0.05010.06990.1435-0.0330.05280.0024-0.310.1038-0.00030.1642-0.03890.01080.1238-0.00350.116711.549740.5223-3.9928
171.2469-0.1303-0.22272.5352-0.76922.3114-0.0270.26490.248-0.28040.0595-0.1293-0.30440.1957-0.02250.1988-0.07180.04430.18790.03450.148612.765241.0213-17.204
180.23290.12010.03320.4660.08060.8872-0.00220.07210.0107-0.05380.0206-0.08160.04780.1081-0.01420.07950.00620.00840.0985-0.00040.08275.656624.0842-6.423
190.86010.3511-0.20410.9225-0.02680.57930.02490.0783-0.0875-0.0218-0.00330.00810.038-0.0484-0.01530.08470.0031-0.00070.087-0.0120.0575-4.963814.9208-4.9288
200.37120.09190.03690.352-0.04920.4063-0.0207-0.00650.04990.01840.0094-0.0199-0.050.02720.00830.06260.00240.00020.0545-0.00430.07836.48432.948726.5288
210.4057-0.0903-0.01940.43610.14770.7560.0026-0.0324-0.00660.0584-0.01050.1120.0512-0.10850.00910.0779-0.0050.00960.07710.01010.0862-15.282216.857237.1202
220.55680.16690.07510.4477-0.02010.3717-0.0112-0.0309-0.0134-0.00110.008-0.0570.02720.0351-0.00210.06550.0160.00530.0519-0.00320.07264.657524.027432.0044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN B AND (RESID 69:87)B0
2X-RAY DIFFRACTION2CHAIN B AND (RESID 88:163)B0
3X-RAY DIFFRACTION3CHAIN B AND (RESID 164:296)B0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 297:371)B0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 372:428)B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 429:445)B0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 69:163)A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 164:296)A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 297:412)A0
10X-RAY DIFFRACTION10CHAIN A AND (RESID 413:445)A0
11X-RAY DIFFRACTION11CHAIN E AND (RESID 69:87)E0
12X-RAY DIFFRACTION12CHAIN E AND (RESID 88:130)E0
13X-RAY DIFFRACTION13CHAIN E AND (RESID 131:163)E0
14X-RAY DIFFRACTION14CHAIN E AND (RESID 164:267)E0
15X-RAY DIFFRACTION15CHAIN E AND (RESID 268:296)E0
16X-RAY DIFFRACTION16CHAIN E AND (RESID 297:333)E0
17X-RAY DIFFRACTION17CHAIN E AND (RESID 334:356)E0
18X-RAY DIFFRACTION18CHAIN E AND (RESID 357:412)E0
19X-RAY DIFFRACTION19CHAIN E AND (RESID 413:445)E0
20X-RAY DIFFRACTION20CHAIN G AND (RESID 69:296)G0
21X-RAY DIFFRACTION21CHAIN G AND (RESID 297:371)G0
22X-RAY DIFFRACTION22CHAIN G AND (RESID 372:445)G0

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