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- PDB-9az1: Crystal structure of PR9465 peroxidase from Pseudomonas rhizosphaerae -

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Basic information

Entry
Database: PDB / ID: 9az1
TitleCrystal structure of PR9465 peroxidase from Pseudomonas rhizosphaerae
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / FERRIDOXIN-LIKE
Function / homology
Function and homology information


ferrochelatase activity / iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / periplasmic space / 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 / OXYGEN MOLECULE / Deferrochelatase
Similarity search - Component
Biological speciesPseudomonas rhizosphaerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,85910
Polymers43,9011
Non-polymers9579
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.552, 94.552, 98.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deferrochelatase / Peroxidase EfeB


Mass: 43901.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas rhizosphaerae (bacteria) / Gene: LT40_09465 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A089YV40, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 5 types, 317 molecules

#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
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 mg/mL protein with 0.1 M Bis-Tris pH 6.5, 1.8 M ammonium sulfate, 2% (v/v) PEG 550 monomethyl ether (MME), cryoprotectant 2% (v/v) PEG 200 and 2% (w/v) glycerol

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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: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30.02 Å / Num. obs: 18809 / % possible obs: 98.1 % / Redundancy: 11.3 % / Biso Wilson estimate: 30.83 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.034 / Net I/σ(I): 20.42
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 986 / CC1/2: 0.871 / Rpim(I) all: 0.215

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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: 2.3→30.02 Å / SU ML: 0.2528 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 23.2431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 1866 9.92 %
Rwork0.2028 16943 -
obs0.2074 18809 92.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 56 308 3403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213162
X-RAY DIFFRACTIONf_angle_d0.44134307
X-RAY DIFFRACTIONf_chiral_restr0.0378457
X-RAY DIFFRACTIONf_plane_restr0.0032578
X-RAY DIFFRACTIONf_dihedral_angle_d8.4442431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.28071310.23491186X-RAY DIFFRACTION86.08
2.36-2.430.3221410.23641284X-RAY DIFFRACTION92.71
2.43-2.510.2571460.2361278X-RAY DIFFRACTION92.71
2.51-2.60.32371500.23371306X-RAY DIFFRACTION94.92
2.6-2.710.33661350.23851302X-RAY DIFFRACTION93.68
2.71-2.830.28481550.23981315X-RAY DIFFRACTION95.15
2.83-2.980.25951480.2241349X-RAY DIFFRACTION95.29
2.98-3.160.27491440.20711327X-RAY DIFFRACTION95.58
3.16-3.410.25451470.20711351X-RAY DIFFRACTION95.6
3.41-3.750.3171100.22681008X-RAY DIFFRACTION71.07
3.75-4.290.18961500.17141323X-RAY DIFFRACTION92.88
4.29-5.40.18071410.15151408X-RAY DIFFRACTION96.51
5.4-30.020.21241680.19331506X-RAY DIFFRACTION97.5
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)
11.247805250180.0323434401633-0.01225747541451.15673751024-0.02098714869531.456157487190.00833380355464-0.01853968117430.135417717194-0.0296628435397-0.0351671084634-0.044592658083-0.3224918688310.153208570450.01960134037980.314066436793-0.001569966543390.01528615152930.229542740335-0.03071799644660.233651202487-24.261.264-0.548
21.26485540813-0.289249117027-0.02922920680841.251397516820.1229579233131.219117252740.07250132392150.05591233491740.019999586356-0.0305028577989-0.09547669138850.0780965913999-0.0643278544784-0.06685401598180.02046978099380.211876657309-0.0187715858696-0.0005503997127080.1537317874250.008130673133120.18227922615-24.485-8.547-8.853
33.2483715148-1.96428367579-0.6462046326082.234415627170.5164592821790.5394857351140.1326631445520.311063007040.17465452484-0.271869830147-0.133654781007-0.168902092387-0.110615528472-0.0822613023280.008807874152720.217036865769-0.00782316732991-0.01285799319660.2271745186670.00995051504470.198883053275-12.691-12.868-23.33
42.64340872428-0.419713204144-0.5906801238343.143928636880.5875255203945.796829511650.2339944994610.4736336972270.0826840145777-0.723572818931-0.2406560021140.0727687435005-0.393713004395-0.142932755647-0.02852815509070.2442037644540.0601605295782-0.03946093737550.294931831851-0.01335003409110.252803634383-13.145-16.27-28.849
51.59557951233-1.207438721350.5260491136142.404943429590.06746664162570.4666008055820.1446033162140.116521222729-0.0899933430745-0.211135863382-0.05542526192170.01690532148680.1039551223310.013953694753-0.08670912606070.174591350844-0.008873541839090.006432216772440.253707350044-0.0536172255330.212878407009-21.311-19.621-18.092
66.729428908132.204033699230.5837605140688.233210538380.6861013000674.205803288440.176690519869-0.007193193219850.435936476623-0.036269263121-0.06814414936080.783146390684-0.631721371873-0.402886446443-0.134613451650.4238005938240.0631146829909-0.05289706266360.287077403472-0.01327511086630.323067358697-35.578.086-13.971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:126 )A44 - 126
2X-RAY DIFFRACTION2( CHAIN A AND RESID 127:237 )A127 - 237
3X-RAY DIFFRACTION3( CHAIN A AND RESID 238:323 )A238 - 323
4X-RAY DIFFRACTION4( CHAIN A AND RESID 324:359 )A324 - 359
5X-RAY DIFFRACTION5( CHAIN A AND RESID 360:411 )A360 - 411
6X-RAY DIFFRACTION6( CHAIN A AND RESID 412:432 )A412 - 432

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