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- PDB-24rq: Crystal structure of Pseudomonas fluorescens peroxidase EfeB -

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Basic information

Entry
Database: PDB / ID: 24rq
TitleCrystal structure of Pseudomonas fluorescens peroxidase EfeB
ComponentsDeferrochelatase
KeywordsOXYGEN BINDING / Pseudomonas / Iron-importing Efe system
Function / homology
Function and homology information


iron import into cell / protoporphyrin ferrochelatase activity / cell envelope / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Deferrochelatase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsOkumura, K. / Ogura, K. / Mikami, B. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25KJ1671 Japan
CitationJournal: To Be Published
Title: Crystal structure of Pseudomonas fluorescens peroxidase EfeB
Authors: Okumura, K. / Ogura, K. / Mikami, B. / Hashimoto, W.
History
DepositionMar 18, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
C: Deferrochelatase
D: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,06557
Polymers178,8894
Non-polymers7,17653
Water14,664814
1
A: Deferrochelatase
D: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,96428
Polymers89,4452
Non-polymers3,51926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-150 kcal/mol
Surface area29620 Å2
MethodPISA
2
B: Deferrochelatase
C: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,10229
Polymers89,4452
Non-polymers3,65727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-250 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.660, 136.660, 217.375
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11D-751-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Deferrochelatase / Peroxidase EfeB


Mass: 44722.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: efeB, NCTC10038_02902 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3M3XL07, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 9 types, 867 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG400, 100 mM Sodium cacodylate trihydrate (pH 6.5), 200 mM Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→49.71 Å / Num. obs: 135483 / % possible obs: 99.8 % / Redundancy: 17.29 % / Biso Wilson estimate: 37.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 28.72
Reflection shellResolution: 2.11→2.23 Å / Redundancy: 17.89 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 0.0359 / Num. unique obs: 21522 / CC1/2: 0.897 / Rrim(I) all: 0.936

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→49.71 Å / SU ML: 0.2233 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 6773 5 %
Rwork0.181 128685 -
obs0.1827 135458 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.24 Å2
Refinement stepCycle: LAST / Resolution: 2.11→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12104 0 450 814 13368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007312893
X-RAY DIFFRACTIONf_angle_d0.917917553
X-RAY DIFFRACTIONf_chiral_restr0.05391849
X-RAY DIFFRACTIONf_plane_restr0.00812325
X-RAY DIFFRACTIONf_dihedral_angle_d15.71924861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.130.27382150.25594071X-RAY DIFFRACTION94.93
2.13-2.160.25772240.23674253X-RAY DIFFRACTION100
2.16-2.180.26332210.22684212X-RAY DIFFRACTION100
2.18-2.210.26272270.22484300X-RAY DIFFRACTION100
2.21-2.240.26832220.22944234X-RAY DIFFRACTION99.98
2.24-2.270.27942250.21884265X-RAY DIFFRACTION99.98
2.27-2.30.25862230.21864231X-RAY DIFFRACTION100
2.3-2.340.25662250.22614273X-RAY DIFFRACTION100
2.34-2.370.28162230.21994238X-RAY DIFFRACTION100
2.37-2.410.2762240.21554272X-RAY DIFFRACTION100
2.41-2.450.24682250.2124260X-RAY DIFFRACTION100
2.45-2.50.25942250.21154277X-RAY DIFFRACTION100
2.5-2.550.26462240.21544263X-RAY DIFFRACTION100
2.55-2.60.27282250.21214267X-RAY DIFFRACTION100
2.6-2.650.23712240.2134269X-RAY DIFFRACTION100
2.65-2.720.2262260.20744282X-RAY DIFFRACTION100
2.72-2.780.24742260.21514300X-RAY DIFFRACTION100
2.78-2.860.26212240.21194263X-RAY DIFFRACTION100
2.86-2.940.25112260.21144277X-RAY DIFFRACTION100
2.94-3.040.25222270.21154320X-RAY DIFFRACTION100
3.04-3.150.26762250.21554280X-RAY DIFFRACTION100
3.15-3.270.26292260.21234285X-RAY DIFFRACTION100
3.27-3.420.2152280.18694339X-RAY DIFFRACTION100
3.42-3.60.19292270.17274303X-RAY DIFFRACTION100
3.6-3.830.1872270.16264317X-RAY DIFFRACTION100
3.83-4.120.17722280.14464329X-RAY DIFFRACTION100
4.12-4.540.16772280.13344349X-RAY DIFFRACTION100
4.54-5.190.16082300.13394362X-RAY DIFFRACTION100
5.19-6.540.19362330.1554429X-RAY DIFFRACTION100
6.54-49.710.17652400.15494565X-RAY DIFFRACTION99.44

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