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- PDB-9qdt: Cytochrome c peroxidase YhjA -

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Basic information

Entry
Database: PDB / ID: 9qdt
TitleCytochrome c peroxidase YhjA
ComponentsProbable cytochrome c peroxidase
KeywordsOXIDOREDUCTASE / cytochrome c / peroxidase / multiheme protein
Function / homology
Function and homology information


hydrogen peroxide metabolic process / anaerobic electron transport chain / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to hydrogen peroxide / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Haem-binding domain / Haem-binding domain / Haem-binding domain / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase Ccp
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.572 Å
AuthorsEinsle, O. / Wuest, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)403222702 Germany
CitationJournal: Biochemistry / Year: 2025
Title: Escherichia coli Triheme Enzyme YhjA: Structure and Reactivity.
Authors: Hewitt, P. / Seidel, J. / Wust, A. / Smith, M. / Maiocco, S.J. / Shternberg, S. / Hoffmann, M. / Spatzal, T. / Gerhardt, S. / Einsle, O. / Elliott, S.J.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 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: Probable cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7169
Polymers46,4121
Non-polymers2,3038
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-108 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.42, 101.42, 134.68
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable cytochrome c peroxidase


Mass: 46412.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yhjA, b3518, JW3486 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37197, cytochrome-c peroxidase

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Non-polymers , 7 types, 55 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 5.1 Å3/Da / Density % sol: 76 % / Description: octagon
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M Na/K tartrate 100 mM HEPES/NaOH 2.5 mM Na2S2O4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.57→82 Å / Num. obs: 23032 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 15.4 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.037 / Net I/σ(I): 17.1
Reflection shellResolution: 2.57→2.69 Å / Redundancy: 15.2 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2759 / CC1/2: 0.785 / Rpim(I) all: 0.359 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.572→81.149 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 17.741 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.299 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2219 1185 5.158 %
Rwork0.1724 21791 -
all0.175 --
obs-22976 99.952 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.266 Å2-0 Å2-0 Å2
2---0.266 Å2-0 Å2
3---0.533 Å2
Refinement stepCycle: LAST / Resolution: 2.572→81.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 152 47 3467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163242
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.8924816
X-RAY DIFFRACTIONr_angle_other_deg0.6441.7987474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.899517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42810557
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.61110158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024164
X-RAY DIFFRACTIONr_gen_planes_other0.010.02812
X-RAY DIFFRACTIONr_nbd_refined0.2980.2858
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.23121
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21731
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.295
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.210
X-RAY DIFFRACTIONr_nbd_other0.1410.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.22
X-RAY DIFFRACTIONr_mcbond_it2.9193.8151667
X-RAY DIFFRACTIONr_mcbond_other2.9193.8151667
X-RAY DIFFRACTIONr_mcangle_it4.3716.862082
X-RAY DIFFRACTIONr_mcangle_other4.3716.8622083
X-RAY DIFFRACTIONr_scbond_it3.7524.1551850
X-RAY DIFFRACTIONr_scbond_other3.6484.1411844
X-RAY DIFFRACTIONr_scangle_it5.7757.4632734
X-RAY DIFFRACTIONr_scangle_other5.6387.4422729
X-RAY DIFFRACTIONr_lrange_it7.12536.3274144
X-RAY DIFFRACTIONr_lrange_other7.08136.3164141
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.572-2.6390.292800.27815830.27916630.9360.9491000.25
2.639-2.7110.29900.25415250.25616150.9510.9581000.215
2.711-2.790.317910.23614790.2415700.9360.9641000.202
2.79-2.8750.271730.22714760.22915490.9440.9681000.193
2.875-2.9690.26740.20914170.21214910.9560.9731000.173
2.969-3.0740.21790.20313780.20414570.9680.9731000.17
3.074-3.1890.281810.19213020.19813830.950.9751000.163
3.189-3.3190.214610.18412830.18513440.9730.9781000.16
3.319-3.4670.257750.18112180.18512930.9570.9791000.154
3.467-3.6360.204580.17811920.1812500.9740.9791000.16
3.636-3.8320.247640.16511140.16911780.9610.9821000.15
3.832-4.0640.216550.1510790.15411340.9730.9861000.139
4.064-4.3430.167520.1310050.13110570.9840.991000.123
4.343-4.690.161570.1259410.1289980.9840.9911000.122
4.69-5.1360.173490.1378660.1399150.9810.9881000.135
5.136-5.740.186410.1498020.1518430.9790.9871000.148
5.74-6.6220.242420.1717080.1747500.9650.9831000.173
6.622-8.0970.178280.1466230.1486510.9840.9861000.153
8.097-11.3940.177200.1335000.1345200.9860.9881000.149
11.394-81.1490.384150.2533000.2583260.9290.95896.62580.27

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