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- PDB-9az0: Crystal crystal of FC2591 peroxidase from Frankia casuarinae -

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Basic information

Entry
Database: PDB / ID: 9az0
TitleCrystal crystal of FC2591 peroxidase from Frankia casuarinae
ComponentsDyp-type peroxidase
KeywordsOXIDOREDUCTASE / FERRIDOXIN-LIKE
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / 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 / OXYGEN MOLECULE / Dyp-type peroxidase
Similarity search - Component
Biological speciesFrankia casuarinae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStogios, P.J. / Skarina, T. / Choolaei, Z. / Yakunin, A. / Savchenko, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Structural and Biochemical Insights into Lignin-Oxidizing Activity of Bacterial Peroxidases against Soluble Substrates and Kraft Lignin.
Authors: Choolaei, Z. / Khusnutdinova, A.N. / Skarina, T. / Stogios, P. / Diep, P. / Lemak, S. / Edwards, E.A. / Savchenko, A. / Yakunin, A.F.
History
DepositionMar 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dyp-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4063
Polymers40,7581
Non-polymers6482
Water12,683704
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.434, 71.639, 76.638
Angle α, β, γ (deg.)90.000, 109.230, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1049-

HOH

21A-1090-

HOH

31A-1206-

HOH

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Components

#1: Protein Dyp-type peroxidase


Mass: 40757.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia casuarinae (bacteria) / Gene: Francci3_2591 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2J9T9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 39.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15 mg/mL protein plus 40 mM zinc acetate, 18% (w/v) Polyethylene glycol (PEG) 3350, cryoprotectant paratone oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 39461 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.13 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.027 / Net I/σ(I): 28.97
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 1922 / CC1/2: 0.888 / Rpim(I) all: 0.221 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→24.12 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1796 1972 5 %
Rwork0.1441 37489 -
obs0.1459 39461 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.71 Å2
Refinement stepCycle: LAST / Resolution: 1.65→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 45 704 3396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682757
X-RAY DIFFRACTIONf_angle_d0.91273765
X-RAY DIFFRACTIONf_chiral_restr0.0558401
X-RAY DIFFRACTIONf_plane_restr0.0087508
X-RAY DIFFRACTIONf_dihedral_angle_d14.3883985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.29221280.27882445X-RAY DIFFRACTION91.24
1.69-1.730.25471410.22872654X-RAY DIFFRACTION98.07
1.73-1.780.23921420.1852687X-RAY DIFFRACTION98.47
1.78-1.840.211390.16192654X-RAY DIFFRACTION98.76
1.84-1.910.20711400.16072657X-RAY DIFFRACTION99.33
1.91-1.980.19351390.15692670X-RAY DIFFRACTION99.43
1.98-2.070.21481420.16582700X-RAY DIFFRACTION99.61
2.07-2.180.20411420.14982708X-RAY DIFFRACTION99.89
2.18-2.320.22681420.1462692X-RAY DIFFRACTION99.93
2.32-2.50.17681420.14082698X-RAY DIFFRACTION100
2.5-2.750.14821420.14332707X-RAY DIFFRACTION100
2.75-3.150.17221430.13832707X-RAY DIFFRACTION100
3.15-3.960.14721440.11922742X-RAY DIFFRACTION99.93
3.96-24.120.1571460.12842768X-RAY DIFFRACTION99.9
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.46710363405-2.52969424420.9543368987232.664159708690.09806491690651.889217921320.01838463222440.05373720134330.136665031304-0.0536139612541-0.07312815625330.0438769163843-0.0968173387575-0.02393576616460.04862766878560.0807359802203-0.02845866102950.03322022363790.1035638986330.04865980454420.07303575013069.60408566406-3.3922383248514.4537371487
24.0779140819-4.606090689842.125437301559.9032018079-4.515683995114.078523497990.0232257856995-0.003972114639110.1719932277130.0653924001691-0.120844572672-0.3343349319510.04909206272380.2960832578030.09588865791620.106461772220.00218750993767-0.0009673522514170.151672941451-0.03189909656670.10931829800922.0728553633-6.7613796314815.5657603819
30.191887452412-0.3329811415510.6599746570651.60328250667-2.294823945774.637959773510.03845247156720.0351482525231-0.0104444726307-0.0233124322395-0.0271914744969-0.0526863007583-0.1248694208620.2896644295330.02546016148370.129369768252-0.02452689230220.008378516166940.19859808957-0.005499965161190.20806540141415.740777155-1.008786466488.20960570815
40.531022028398-0.0929705332516-0.4038213288651.53086835667-0.4626240560760.827919156315-0.0120446654565-0.0162090065215-0.117486302169-0.0549871528942-0.00709184229810.0550272520370.1951083202830.03207920105470.01435474606580.149757846704-0.0031005728507-0.006775104000230.14843237384-0.001050479059470.1645664618595.8717590297-13.257965713519.4851961327
51.82240863402-0.5517541992471.258218258231.4534230135-1.527578792161.972148563820.05867625634290.050651497811-0.0179754039895-0.121840892315-0.0759397550497-0.1360083706130.1195660665220.1779926121110.02000069457970.1898540329660.01925977748790.01593754698330.169412702845-0.01961055323020.16296541495112.2130630955-7.827528330465.11051449743
61.5937413970.963304400752-0.7022702328761.793316451860.6438023816261.654175437830.0620448225248-0.08749319186640.117910511236-0.05554518573380.0214346703429-0.0709861477674-0.0965800667715-0.152077399918-0.08990526310490.1761258308230.0268270746995-0.000552177800790.162504050330.0106150036710.175671577871-9.378651125175.85217799098.38542104132
74.82068675464-0.07146118799491.826965768370.637128925871-0.1206337019671.74873211673-0.123488779331-0.1849827307580.4279293639610.07874703941980.0283728438202-0.0307034144794-0.0994095881099-0.05348140228350.09746719906880.13730213562-0.01444829870810.01666133614050.1119810735050.00545585176610.1315543221191.67365097915-1.2389616738224.5952837674
82.93695890413-0.377062792689-0.2974754371154.202676275232.476125937834.29007381352-0.0217611537840.3489378544250.0233923662326-0.249940285358-0.03110198543580.148473779608-0.323326626911-0.1739708284960.08199718630970.1256959328550.00429824115194-0.006291824124770.1860164712920.03148475007350.116882447826-22.8290773192-0.53000569280714.9250737956
91.83921069209-0.211856802821-1.703329648850.186870555044-0.1450655395342.09104461365-0.04196854533840.0506300165207-0.03928424819060.00968237309135-0.01108095872340.09296721555930.106873913413-0.05329255693240.05923817150740.152202882347-0.0001451313368530.000621223482870.1356006696910.006753007364210.165210841494-14.62323514-4.6027581448220.5437749895
104.447907240170.4045501445140.6779136253350.4404559109370.1314717453380.292911572687-0.0189810794617-0.0840425533169-0.09558407377550.01998047166080.01537407607460.03279519686020.03804453825670.00413694290329-0.006398341948620.14415792097-0.0002158925703820.001867437478930.1153388287610.004412734086380.1088596959151.17448012342-8.8566317751521.7631801875
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 55 )30 - 551 - 26
22chain 'A' and (resid 56 through 78 )56 - 7827 - 49
33chain 'A' and (resid 79 through 111 )79 - 11150 - 82
44chain 'A' and (resid 112 through 150 )112 - 15083 - 121
55chain 'A' and (resid 151 through 178 )151 - 178122 - 149
66chain 'A' and (resid 179 through 198 )179 - 198150 - 169
77chain 'A' and (resid 199 through 238 )199 - 238170 - 209
88chain 'A' and (resid 239 through 275 )239 - 275210 - 246
99chain 'A' and (resid 276 through 330 )276 - 330247 - 301
1010chain 'A' and (resid 331 through 389 )331 - 389302 - 360

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