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- PDB-9h1m: Recombinant ferric horseradish peroxidase C1A -

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Basic information

Entry
Database: PDB / ID: 9h1m
TitleRecombinant ferric horseradish peroxidase C1A
ComponentsPeroxidase C1A
KeywordsOXIDOREDUCTASE / Horseradish Peroxidase / Ferric / oxidoreductases / Heme
Function / homology
Function and homology information


peroxidase / lactoperoxidase activity / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Plant peroxidase / Secretory peroxidase / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase C1A
Similarity search - Component
Biological speciesArmoracia rusticana (horseradish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsNesa, M.L. / Mandal, S.K. / Toelzer, C. / Humer, D. / Moody, P.C.E. / Berger, I. / Spadiut, O. / Raven, E.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme Trust2024-263/4 United Kingdom
CitationJournal: J.Biol.Inorg.Chem. / Year: 2025
Title: Crystal structure of ferric recombinant horseradish peroxidase.
Authors: Nesa, M.L. / Mandal, S.K. / Toelzer, C. / Humer, D. / Moody, P.C.E. / Berger, I. / Spadiut, O. / Raven, E.L.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxidase C1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,18310
Polymers34,0791
Non-polymers1,1049
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-4 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.157, 67.061, 117.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peroxidase C1A


Mass: 34079.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Armoracia rusticana (horseradish) / Gene: PRXC1A, HPRC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00433, peroxidase

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Non-polymers , 5 types, 149 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) PEG 1500, 100 mM SPG (2:7:7, succinic acid:sodium hydrogen phosphate:glycine buffer pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.63→58.2 Å / Num. obs: 37103 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.02 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.115 / Net I/σ(I): 5.4
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 2.1 % / Num. unique obs: 1850 / CC1/2: 0.343 / % possible all: 93.6

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
Coot0.9.8model building
PHASERphasing
PHENIX1.21refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→58.2 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 1903 5.25 %
Rwork0.1698 --
obs0.1709 36260 89.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→58.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 70 140 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052491
X-RAY DIFFRACTIONf_angle_d0.8763396
X-RAY DIFFRACTIONf_dihedral_angle_d13.381900
X-RAY DIFFRACTIONf_chiral_restr0.042380
X-RAY DIFFRACTIONf_plane_restr0.008448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.3181260.31622206X-RAY DIFFRACTION82
1.67-1.720.3299980.30372000X-RAY DIFFRACTION75
1.72-1.770.26391080.23832275X-RAY DIFFRACTION84
1.77-1.820.25091340.21962665X-RAY DIFFRACTION98
1.82-1.890.23211350.22212207X-RAY DIFFRACTION83
1.89-1.960.22741140.19952112X-RAY DIFFRACTION78
1.97-2.050.23321620.15972659X-RAY DIFFRACTION99
2.05-2.160.17131360.14682333X-RAY DIFFRACTION87
2.16-2.30.17631320.13992521X-RAY DIFFRACTION92
2.3-2.480.15851560.14372724X-RAY DIFFRACTION100
2.48-2.720.18371500.15252537X-RAY DIFFRACTION93
2.73-3.120.18931520.16262764X-RAY DIFFRACTION99
3.12-3.930.21011400.16412441X-RAY DIFFRACTION88
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)
10.0903-0.0464-0.08190.167-0.12710.16830.03420.3302-0.0393-0.1796-0.0404-0.00610.09990.034700.3012-0.00130.00020.2656-0.04450.237510.999113.090533.6762
20.01380.0363-0.05170.1261-0.0610.1754-0.00350.23530.00330.0704-0.06360.0770.1733-0.0533-00.2105-0.0089-0.01050.2791-0.02330.2151.764323.0142.6938
30.1372-0.02690.08170.1214-0.0317-0.00690.0085-0.1423-0.05970.0949-0.12720.0762-0.02550.01270.00010.2438-0.02850.02090.20230.01110.22567.671716.215656.3181
40.23490.2570.0560.3651-0.29860.2625-0.09380.0756-0.15830.222-0.07460.32470.254-0.1773-00.2581-0.0128-0.00850.2404-0.01210.2494.213212.292844.3583
5-0.0301-0.05220.12050.1989-0.01360.0585-0.01760.0258-0.0812-0.0252-0.1099-0.06050.0840.046600.24580.0015-0.00520.25240.01650.217211.877518.70740.366
60.084-0.05540.07060.19280.0140.0856-0.004-0.06680.02160.2232-0.0405-0.0507-0.028-0.019600.2082-0.00590.00060.207-0.0090.247712.073834.011854.6606
70.0437-0.030.0190.2193-0.0911-0.0295-0.0297-0.00830.0590.02760.00780.07940.0180.044-00.20230.00650.00340.2415-0.01280.25470.138836.889447.4155
80.0420.07940.10010.3263-0.09270.20440.01960.03810.01660.14980.01320.1013-0.0511-0.0104-00.22470.00310.0210.26430.00530.2771-9.192143.873550.7176
90.2428-0.14880.06470.3472-0.00920.14710.02110.01790.0732-0.0704-0.05850.0624-0.1191-0.019100.22890.0031-0.00820.2310.01570.23214.980743.12740.3608
10-0.03330.00840.06270.14880.06110.03580.05560.0288-0.079-0.1091-0.0454-0.1310.21010.130900.21040.01560.00720.23670.03320.194614.980631.604136.6703
110.0272-0.0480.05810.0477-0.07540.1402-0.03020.01440.05240.1452-0.05570.04790.10430.028100.2892-0.00850.01730.25950.00560.247514.45919.6649.8666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 159 )
7X-RAY DIFFRACTION7chain 'A' and (resid 160 through 185 )
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 220 )
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 269 )
10X-RAY DIFFRACTION10chain 'A' and (resid 270 through 286 )
11X-RAY DIFFRACTION11chain 'A' and (resid 287 through 306 )

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